GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in CHOL-TP
Cholangiocarcinoma (Primary solid tumor)
28 January 2016 | analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1XK8DXD
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in CHOL-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1XK8DXD
Overview
Introduction

This pipeline performs Gene Set Enrichment Analysis (GSEA) using The Broad Institute GSEA tool with MSigDB - Class2: Canonical Pathways gene sets. For a given phenotype subtype, it shows what pathways are significantly enriched in each subtype by comparing gene expression profiles between subtypes. Here, the phenotype is mRNAseq_cNMF subtypes having more than three samples and the input expression file "CHOL-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt" is generated in the pipeline mRNAseq_Preprocess in the stddata run. This pipeline has the following features:

1. For each subtype, calculates enrichment scores (ES) using signal to noise (S2N) that checks similarity between subtypes in expression level then calculates p values through permutation test.

2. Lists pathways significantly enriched in each phenotype subtype and their enrichment scores (ES).

3. Lists top 20 core genes enriched in each significant gene set and their enrichment scores (ES).

4. Checks if the top core genes are up-regulated or down-regulated.

5. Checks if the top core genes are high expressed or low expressed.

6. Checks if the top core genes are significantly differently expressed genes.

Summary

Table 1. Get Full Table basic data info

basic data info
Number of Gene Sets: 719
Number of samples: 36
Original number of Gene Sets: 1320
Maximum gene set size: 933

Table 2. Get Full Table pheno data info

phenotype info
pheno.type: 1 - 6 :[ clus1 ] 6
pheno.type: 2 - 6 :[ clus2 ] 4
pheno.type: 3 - 6 :[ clus3 ] 5
pheno.type: 4 - 6 :[ clus4 ] 6
pheno.type: 5 - 6 :[ clus5 ] 9
pheno.type: 6 - 6 :[ clus6 ] 6

For the expression subtypes of 18131 genes in 37 samples, GSEA found enriched gene sets in each cluster using 36 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

- clus1

- Top enriched gene sets are KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM, KEGG UBIQUITIN MEDIATED PROTEOLYSIS, KEGG THYROID CANCER, BIOCARTA GPCR PATHWAY, PID ER NONGENOMIC PATHWAY, PID MET PATHWAY, PID CDC42 PATHWAY, PID RETINOIC ACID PATHWAY, PID DELTANP63PATHWAY, PID A6B1 A6B4 INTEGRIN PATHWAY

- And common core enriched genes are MAPK3, RXRG, PRKCG, CTNNB1, LEF1, NTRK1, PPARG, RET, TCF7, TCF7L2

- clus2

- Top enriched gene sets are KEGG CITRATE CYCLE TCA CYCLE, KEGG OXIDATIVE PHOSPHORYLATION, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG ALZHEIMERS DISEASE, KEGG PARKINSONS DISEASE, KEGG HUNTINGTONS DISEASE, ST GAQ PATHWAY, PID MTOR 4PATHWAY, REACTOME TRANSLATION, REACTOME PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE

- And common core enriched genes are ACO2, ATP5A1, ATP5B, ATP5G1, CS, CYC1, C18orf55, CHCHD4, COQ2, DNAJC19

- clus3

- Top enriched gene sets are KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION, KEGG CHEMOKINE SIGNALING PATHWAY, KEGG ENDOCYTOSIS, KEGG MTOR SIGNALING PATHWAY, KEGG APOPTOSIS, KEGG CELL ADHESION MOLECULES CAMS, KEGG ANTIGEN PROCESSING AND PRESENTATION, KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY, KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY, KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY

- And common core enriched genes are FYN, IKBKB, PIK3CD, PRKCB, SYK, CASP8, CXCL10, CYLD, DDX58, DHX58

- clus4

- Top enriched gene sets are KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, KEGG GLUTATHIONE METABOLISM, KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM, KEGG RIBOSOME, KEGG SPLICEOSOME, KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT, BIOCARTA PROTEASOME PATHWAY, REACTOME ER PHAGOSOME PATHWAY, REACTOME MEMBRANE TRAFFICKING, REACTOME P53 INDEPENDENT G1 S DNA DAMAGE CHECKPOINT

- And common core enriched genes are NQO1, OAZ1, OAZ3, ODC1, PSMA4, PSMA5, PSMA6, PSMB10, PSMB2, PSMB3

- clus5

- Top enriched gene sets are KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG CITRATE CYCLE TCA CYCLE, KEGG PENTOSE PHOSPHATE PATHWAY, KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG FATTY ACID METABOLISM, KEGG STEROID HORMONE BIOSYNTHESIS, KEGG PURINE METABOLISM, KEGG PYRIMIDINE METABOLISM, KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM

- And common core enriched genes are ABCA1, ABCB4, ACADM, ACOX1, ACSL1, AGT, ALAS1, ANGPTL4, ANKRD1, APOA1

- clus6

- Top enriched gene sets are KEGG NOTCH SIGNALING PATHWAY, ST ERK1 ERK2 MAPK PATHWAY, PID INTEGRIN3 PATHWAY, PID RHOA REG PATHWAY, PID NECTIN PATHWAY, PID TGFBRPATHWAY, REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS, REACTOME PRE NOTCH TRANSCRIPTION AND TRANSLATION, REACTOME PRE NOTCH EXPRESSION AND PROCESSING, REACTOME NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION

- And common core enriched genes are SKIL, SMAD7, SMURF2, NCOR2, MAML2, MAML3, MAMLD1, CTGF, SMAD4, ZFYVE9

Results
Subtype clus1 enriched pathways

Table 3. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus1. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM | 74 | genes.ES.table | 0.49 | 1.7 | 0.002 | 1 | 0.87 | 0.43 | 0.29 | 0.31 | 1 | 0.72
KEGG UBIQUITIN MEDIATED PROTEOLYSIS | 134 | genes.ES.table | 0.26 | 1.6 | 0.031 | 1 | 0.93 | 0.44 | 0.41 | 0.26 | 1 | 0.74
KEGG THYROID CANCER | 29 | genes.ES.table | 0.54 | 1.8 | 0.0044 | 1 | 0.61 | 0.31 | 0.2 | 0.25 | 1 | 0.6
BIOCARTA GPCR PATHWAY | 32 | genes.ES.table | 0.46 | 1.5 | 0.047 | 1 | 0.98 | 0.62 | 0.39 | 0.38 | 1 | 0.77
PID ER NONGENOMIC PATHWAY | 41 | genes.ES.table | 0.53 | 1.5 | 0.042 | 1 | 0.99 | 0.63 | 0.33 | 0.42 | 1 | 0.8
PID MET PATHWAY | 79 | genes.ES.table | 0.34 | 1.6 | 0.042 | 1 | 0.95 | 0.46 | 0.39 | 0.28 | 1 | 0.74
PID CDC42 PATHWAY | 70 | genes.ES.table | 0.32 | 1.4 | 0.093 | 1 | 0.99 | 0.49 | 0.39 | 0.3 | 1 | 0.78
PID RETINOIC ACID PATHWAY | 30 | genes.ES.table | 0.54 | 1.7 | 0.0076 | 1 | 0.84 | 0.5 | 0.26 | 0.37 | 1 | 0.75
PID DELTANP63PATHWAY | 46 | genes.ES.table | 0.52 | 1.4 | 0.065 | 1 | 0.99 | 0.46 | 0.28 | 0.33 | 1 | 0.79
PID A6B1 A6B4 INTEGRIN PATHWAY | 46 | genes.ES.table | 0.45 | 1.4 | 0.083 | 1 | 1 | 0.2 | 0.15 | 0.17 | 1 | 0.77

genes ES table in pathway: KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM

Table S1. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | PPARG | PPARG | PPARG | 469 | 0.57 | 0.12 | YES
2 | NTRK1 | NTRK1 | NTRK1 | 1055 | 0.42 | 0.19 | YES
3 | RXRG | RXRG | RXRG | 1126 | 0.4 | 0.29 | YES
4 | TCF7 | TCF7 | TCF7 | 1267 | 0.38 | 0.38 | YES
5 | LEF1 | LEF1 | LEF1 | 2057 | 0.28 | 0.4 | YES
6 | CTNNB1 | CTNNB1 | CTNNB1 | 2340 | 0.26 | 0.45 | YES
7 | TCF7L2 | TCF7L2 | TCF7L2 | 2751 | 0.23 | 0.49 | YES
8 | MAPK3 | MAPK3 | MAPK3 | 3551 | 0.18 | 0.49 | YES
9 | RET | RET | RET | 3581 | 0.18 | 0.54 | YES
10 | KRAS | KRAS | KRAS | 5151 | 0.12 | 0.48 | NO
11 | MAPK1 | MAPK1 | MAPK1 | 6964 | 0.068 | 0.4 | NO
12 | BRAF | BRAF | BRAF | 7026 | 0.066 | 0.41 | NO
13 | RXRA | RXRA | RXRA | 7543 | 0.053 | 0.39 | NO
14 | TFG | TFG | TFG | 7554 | 0.053 | 0.41 | NO
15 | HRAS | HRAS | HRAS | 8060 | 0.04 | 0.39 | NO
16 | MAP2K1 | MAP2K1 | MAP2K1 | 9340 | 0.013 | 0.32 | NO
17 | TPM3 | TPM3 | TPM3 | 9649 | 0.0061 | 0.3 | NO
18 | CCDC6 | CCDC6 | CCDC6 | 10656 | -0.016 | 0.25 | NO
19 | PAX8 | PAX8 | PAX8 | 10829 | -0.02 | 0.25 | NO
20 | NCOA4 | NCOA4 | NCOA4 | 11044 | -0.024 | 0.24 | NO
21 | TCF7L1 | TCF7L1 | TCF7L1 | 11143 | -0.026 | 0.24 | NO
22 | CCND1 | CCND1 | CCND1 | 11245 | -0.028 | 0.25 | NO
23 | NRAS | NRAS | NRAS | 11600 | -0.036 | 0.24 | NO
24 | CDH1 | CDH1 | CDH1 | 12179 | -0.049 | 0.22 | NO
25 | MAP2K2 | MAP2K2 | MAP2K2 | 12248 | -0.05 | 0.22 | NO
26 | TPR | TPR | TPR | 13130 | -0.071 | 0.19 | NO
27 | RXRB | RXRB | RXRB | 13142 | -0.072 | 0.21 | NO
28 | MYC | MYC | MYC | 14445 | -0.11 | 0.17 | NO
29 | TP53 | TP53 | TP53 | 15113 | -0.14 | 0.17 | NO

Figure S1. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM.

Figure S2. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG UBIQUITIN MEDIATED PROTEOLYSIS

Table S2. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | VDR | VDR | VDR | 496 | 0.56 | 0.083 | YES
2 | RARB | RARB | RARB | 890 | 0.45 | 0.15 | YES
3 | RBP1 | RBP1 | RBP1 | 1025 | 0.43 | 0.23 | YES
4 | PRKCG | PRKCG | PRKCG | 1032 | 0.42 | 0.31 | YES
5 | RXRG | RXRG | RXRG | 1126 | 0.4 | 0.39 | YES
6 | MAPK8 | MAPK8 | MAPK8 | 2291 | 0.27 | 0.38 | YES
7 | MNAT1 | MNAT1 | MNAT1 | 2587 | 0.24 | 0.41 | YES
8 | NRIP1 | NRIP1 | NRIP1 | 3534 | 0.18 | 0.39 | YES
9 | MAPK3 | MAPK3 | MAPK3 | 3551 | 0.18 | 0.43 | YES
10 | NCOA2 | NCOA2 | NCOA2 | 3637 | 0.18 | 0.46 | YES
11 | CDK1 | CDK1 | CDK1 | 3882 | 0.17 | 0.48 | YES
12 | KAT2B | KAT2B | KAT2B | 4309 | 0.15 | 0.48 | YES
13 | HDAC1 | HDAC1 | HDAC1 | 4422 | 0.15 | 0.51 | YES
14 | AKT1 | AKT1 | AKT1 | 4692 | 0.14 | 0.52 | YES
15 | RARG | RARG | RARG | 4732 | 0.14 | 0.54 | YES
16 | NCOA1 | NCOA1 | NCOA1 | 5920 | 0.096 | 0.5 | NO
17 | PRKCA | PRKCA | PRKCA | 6132 | 0.09 | 0.5 | NO
18 | NCOA3 | NCOA3 | NCOA3 | 6637 | 0.076 | 0.49 | NO
19 | MAPK1 | MAPK1 | MAPK1 | 6964 | 0.068 | 0.48 | NO
20 | RXRA | RXRA | RXRA | 7543 | 0.053 | 0.46 | NO
21 | CREBBP | CREBBP | CREBBP | 7829 | 0.046 | 0.46 | NO
22 | EP300 | EP300 | EP300 | 8470 | 0.031 | 0.43 | NO
23 | PRKACA | PRKACA | PRKACA | 10370 | -0.0095 | 0.32 | NO
24 | MAPK14 | MAPK14 | MAPK14 | 11262 | -0.029 | 0.28 | NO
25 | NCOR2 | NCOR2 | NCOR2 | 11622 | -0.037 | 0.27 | NO
26 | CCNH | CCNH | CCNH | 12854 | -0.064 | 0.21 | NO
27 | RXRB | RXRB | RXRB | 13142 | -0.072 | 0.21 | NO
28 | HDAC3 | HDAC3 | HDAC3 | 13206 | -0.073 | 0.22 | NO
29 | RARA | RARA | RARA | 13304 | -0.076 | 0.23 | NO
30 | CDK7 | CDK7 | CDK7 | 15654 | -0.17 | 0.14 | NO

Figure S3. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG UBIQUITIN MEDIATED PROTEOLYSIS.

Figure S4. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG UBIQUITIN MEDIATED PROTEOLYSIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG THYROID CANCER

Table S3. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | PIP5K1B | PIP5K1B | PIP5K1B | 302 | 0.65 | 0.041 | YES
2 | CALML3 | CALML3 | CALML3 | 381 | 0.6 | 0.09 | YES
3 | ITPR1 | ITPR1 | ITPR1 | 417 | 0.58 | 0.14 | YES
4 | DGKB | DGKB | DGKB | 486 | 0.56 | 0.18 | YES
5 | INPP4B | INPP4B | INPP4B | 522 | 0.55 | 0.23 | YES
6 | DGKI | DGKI | DGKI | 678 | 0.5 | 0.27 | YES
7 | PRKCG | PRKCG | PRKCG | 1032 | 0.42 | 0.28 | YES
8 | PLCB4 | PLCB4 | PLCB4 | 1341 | 0.37 | 0.3 | YES
9 | PIK3C2G | PIK3C2G | PIK3C2G | 1750 | 0.32 | 0.31 | YES
10 | DGKG | DGKG | DGKG | 2021 | 0.29 | 0.32 | YES
11 | CALM1 | CALM1 | CALM1 | 2342 | 0.26 | 0.32 | YES
12 | ITPKA | ITPKA | ITPKA | 2431 | 0.26 | 0.34 | YES
13 | PIK3CG | PIK3CG | PIK3CG | 2550 | 0.24 | 0.36 | YES
14 | ITPKB | ITPKB | ITPKB | 2606 | 0.24 | 0.37 | YES
15 | PLCE1 | PLCE1 | PLCE1 | 2730 | 0.23 | 0.39 | YES
16 | PIK3R3 | PIK3R3 | PIK3R3 | 2846 | 0.22 | 0.4 | YES
17 | DGKE | DGKE | DGKE | 2930 | 0.22 | 0.42 | YES
18 | DGKH | DGKH | DGKH | 2972 | 0.22 | 0.43 | YES
19 | CDS1 | CDS1 | CDS1 | 3452 | 0.19 | 0.42 | YES
20 | ITPK1 | ITPK1 | ITPK1 | 3634 | 0.18 | 0.43 | YES
21 | IPPK | IPPK | IPPK | 3871 | 0.17 | 0.43 | YES
22 | PIK3CD | PIK3CD | PIK3CD | 3972 | 0.16 | 0.44 | YES
23 | PIK3CA | PIK3CA | PIK3CA | 4081 | 0.16 | 0.45 | YES
24 | ITPR2 | ITPR2 | ITPR2 | 4187 | 0.16 | 0.46 | YES
25 | INPP1 | INPP1 | INPP1 | 4223 | 0.15 | 0.47 | YES
26 | PIP4K2A | PIP4K2A | PIP4K2A | 4362 | 0.15 | 0.47 | YES
27 | DGKA | DGKA | DGKA | 4436 | 0.15 | 0.48 | YES
28 | PLCB2 | PLCB2 | PLCB2 | 4775 | 0.13 | 0.48 | YES
29 | DGKQ | DGKQ | DGKQ | 4929 | 0.13 | 0.48 | YES
30 | PIK3R5 | PIK3R5 | PIK3R5 | 5119 | 0.12 | 0.48 | YES
31 | DGKZ | DGKZ | DGKZ | 5129 | 0.12 | 0.49 | YES
32 | PLCB1 | PLCB1 | PLCB1 | 5282 | 0.12 | 0.49 | YES
33 | PIK3C2A | PIK3C2A | PIK3C2A | 5587 | 0.11 | 0.48 | NO
34 | PLCG1 | PLCG1 | PLCG1 | 5675 | 0.1 | 0.49 | NO
35 | PLCB3 | PLCB3 | PLCB3 | 5958 | 0.095 | 0.48 | NO
36 | PRKCA | PRKCA | PRKCA | 6132 | 0.09 | 0.48 | NO
37 | ITPR3 | ITPR3 | ITPR3 | 6252 | 0.086 | 0.48 | NO
38 | INPP5D | INPP5D | INPP5D | 7007 | 0.067 | 0.44 | NO
39 | IMPA2 | IMPA2 | IMPA2 | 7385 | 0.057 | 0.43 | NO
40 | PIK3CB | PIK3CB | PIK3CB | 7508 | 0.054 | 0.43 | NO
41 | PTEN | PTEN | PTEN | 7787 | 0.047 | 0.42 | NO
42 | INPP5A | INPP5A | INPP5A | 7819 | 0.046 | 0.42 | NO
43 | PIP5K1C | PIP5K1C | PIP5K1C | 7928 | 0.043 | 0.42 | NO
44 | IMPA1 | IMPA1 | IMPA1 | 8008 | 0.041 | 0.41 | NO
45 | CALM3 | CALM3 | CALM3 | 8202 | 0.037 | 0.41 | NO
46 | PLCD1 | PLCD1 | PLCD1 | 8229 | 0.036 | 0.41 | NO
47 | INPPL1 | INPPL1 | INPPL1 | 8273 | 0.035 | 0.41 | NO
48 | SYNJ2 | SYNJ2 | SYNJ2 | 8422 | 0.032 | 0.4 | NO
49 | DGKD | DGKD | DGKD | 8587 | 0.028 | 0.4 | NO
50 | PIKFYVE | PIKFYVE | PIKFYVE | 8822 | 0.023 | 0.39 | NO
51 | INPP4A | INPP4A | INPP4A | 8933 | 0.021 | 0.38 | NO
52 | PIK3C2B | PIK3C2B | PIK3C2B | 9468 | 0.01 | 0.35 | NO
53 | OCRL | OCRL | OCRL | 9589 | 0.0073 | 0.35 | NO
54 | PLCG2 | PLCG2 | PLCG2 | 9669 | 0.0055 | 0.34 | NO
55 | INPP5E | INPP5E | INPP5E | 9683 | 0.0052 | 0.34 | NO
56 | PI4KA | PI4KA | PI4KA | 9786 | 0.0027 | 0.34 | NO
57 | CDIPT | CDIPT | CDIPT | 9907 | 0.0003 | 0.33 | NO
58 | PIP4K2B | PIP4K2B | PIP4K2B | 9959 | -0.0007 | 0.33 | NO
59 | CALM2 | CALM2 | CALM2 | 10480 | -0.012 | 0.3 | NO
60 | INPP5K | INPP5K | INPP5K | 10573 | -0.014 | 0.3 | NO
61 | PIK3R1 | PIK3R1 | PIK3R1 | 11051 | -0.024 | 0.27 | NO
62 | PIK3C3 | PIK3C3 | PIK3C3 | 11229 | -0.028 | 0.26 | NO
63 | PRKCB | PRKCB | PRKCB | 11448 | -0.033 | 0.26 | NO
64 | PIP5K1A | PIP5K1A | PIP5K1A | 11961 | -0.044 | 0.23 | NO
65 | PIP4K2C | PIP4K2C | PIP4K2C | 12546 | -0.057 | 0.2 | NO
66 | INPP5B | INPP5B | INPP5B | 12959 | -0.067 | 0.19 | NO
67 | PIK3R2 | PIK3R2 | PIK3R2 | 13077 | -0.07 | 0.19 | NO
68 | SYNJ1 | SYNJ1 | SYNJ1 | 13362 | -0.078 | 0.18 | NO
69 | PI4KB | PI4KB | PI4KB | 13690 | -0.087 | 0.17 | NO
70 | CALML6 | CALML6 | CALML6 | 13880 | -0.093 | 0.16 | NO
71 | CDS2 | CDS2 | CDS2 | 14102 | -0.1 | 0.16 | NO
72 | INPP5J | INPP5J | INPP5J | 15427 | -0.16 | 0.1 | NO
73 | PLCD3 | PLCD3 | PLCD3 | 15446 | -0.16 | 0.12 | NO
74 | PLCD4 | PLCD4 | PLCD4 | 17249 | -0.36 | 0.048 | NO

Figure S5. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG THYROID CANCER.

Figure S6. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG THYROID CANCER, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA GPCR PATHWAY

Table S4. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | GJB6 | GJB6 | GJB6 | 136 | 0.77 | 0.049 | YES
2 | GJB2 | GJB2 | GJB2 | 304 | 0.65 | 0.088 | YES
3 | GJA1 | GJA1 | GJA1 | 434 | 0.58 | 0.12 | YES
4 | TPD52L1 | TPD52L1 | TPD52L1 | 630 | 0.52 | 0.15 | YES
5 | VPS37D | VPS37D | VPS37D | 1127 | 0.4 | 0.15 | YES
6 | GJA3 | GJA3 | GJA3 | 1662 | 0.33 | 0.15 | YES
7 | GJB7 | GJB7 | GJB7 | 1723 | 0.32 | 0.17 | YES
8 | AP1S2 | AP1S2 | AP1S2 | 1786 | 0.31 | 0.19 | YES
9 | AP1M2 | AP1M2 | AP1M2 | 1799 | 0.31 | 0.21 | YES
10 | GJB3 | GJB3 | GJB3 | 1971 | 0.29 | 0.22 | YES
11 | SEC24D | SEC24D | SEC24D | 2368 | 0.26 | 0.22 | YES
12 | SNX9 | SNX9 | SNX9 | 2663 | 0.24 | 0.22 | YES
13 | CHMP2B | CHMP2B | CHMP2B | 2717 | 0.23 | 0.24 | YES
14 | SEC23A | SEC23A | SEC23A | 3447 | 0.19 | 0.21 | YES
15 | VTA1 | VTA1 | VTA1 | 3459 | 0.19 | 0.22 | YES
16 | CLTCL1 | CLTCL1 | CLTCL1 | 3492 | 0.19 | 0.23 | YES
17 | TBC1D8B | TBC1D8B | TBC1D8B | 3556 | 0.18 | 0.24 | YES
18 | GJA9 | GJA9 | GJA9 | 3736 | 0.18 | 0.25 | YES
19 | SH3GL2 | SH3GL2 | SH3GL2 | 3869 | 0.17 | 0.25 | YES
20 | GJB4 | GJB4 | GJB4 | 4105 | 0.16 | 0.25 | YES
21 | SH3D19 | SH3D19 | SH3D19 | 4281 | 0.15 | 0.25 | YES
22 | CPD | CPD | CPD | 4322 | 0.15 | 0.26 | YES
23 | AP4B1 | AP4B1 | AP4B1 | 4360 | 0.15 | 0.27 | YES
24 | AP1S1 | AP1S1 | AP1S1 | 4398 | 0.15 | 0.28 | YES
25 | GJC2 | GJC2 | GJC2 | 4427 | 0.15 | 0.29 | YES
26 | VPS36 | VPS36 | VPS36 | 4452 | 0.14 | 0.3 | YES
27 | GJA5 | GJA5 | GJA5 | 4547 | 0.14 | 0.3 | YES
28 | SEC13 | SEC13 | SEC13 | 4791 | 0.13 | 0.3 | YES
29 | GJD4 | GJD4 | GJD4 | 4900 | 0.13 | 0.3 | YES
30 | PUM1 | PUM1 | PUM1 | 5055 | 0.12 | 0.3 | YES
31 | COPB2 | COPB2 | COPB2 | 5065 | 0.12 | 0.31 | YES
32 | ARRB1 | ARRB1 | ARRB1 | 5127 | 0.12 | 0.32 | YES
33 | YIPF6 | YIPF6 | YIPF6 | 5199 | 0.12 | 0.32 | YES
34 | NECAP1 | NECAP1 | NECAP1 | 5357 | 0.11 | 0.32 | YES
35 | AP3S1 | AP3S1 | AP3S1 | 5459 | 0.11 | 0.32 | YES
36 | GJB5 | GJB5 | GJB5 | 5556 | 0.11 | 0.33 | YES
37 | PIK3C2A | PIK3C2A | PIK3C2A | 5587 | 0.11 | 0.33 | YES
38 | GJA4 | GJA4 | GJA4 | 5636 | 0.1 | 0.34 | YES
39 | MYO6 | MYO6 | MYO6 | 5772 | 0.1 | 0.34 | YES
40 | ARCN1 | ARCN1 | ARCN1 | 6164 | 0.089 | 0.32 | YES
41 | CHMP5 | CHMP5 | CHMP5 | 6241 | 0.087 | 0.33 | YES
42 | AP1B1 | AP1B1 | AP1B1 | 6350 | 0.084 | 0.33 | YES
43 | FTL | FTL | FTL | 6429 | 0.082 | 0.33 | YES
44 | SNAP23 | SNAP23 | SNAP23 | 6523 | 0.079 | 0.33 | YES
45 | VPS4A | VPS4A | VPS4A | 6568 | 0.078 | 0.33 | YES
46 | SAR1B | SAR1B | SAR1B | 6593 | 0.078 | 0.34 | YES
47 | IGF2R | IGF2R | IGF2R | 6649 | 0.076 | 0.34 | YES
48 | SRC | SRC | SRC | 6743 | 0.073 | 0.34 | YES
49 | GJC1 | GJC1 | GJC1 | 6838 | 0.07 | 0.34 | YES
50 | COPB1 | COPB1 | COPB1 | 6894 | 0.069 | 0.34 | YES
51 | GAK | GAK | GAK | 6907 | 0.069 | 0.35 | YES
52 | CTSZ | CTSZ | CTSZ | 7088 | 0.065 | 0.34 | NO
53 | STAM2 | STAM2 | STAM2 | 7222 | 0.061 | 0.34 | NO
54 | COPG | COPG | COPG | 7587 | 0.052 | 0.32 | NO
55 | TFRC | TFRC | TFRC | 7835 | 0.045 | 0.31 | NO
56 | DNM2 | DNM2 | DNM2 | 7851 | 0.045 | 0.31 | NO
57 | SEC24B | SEC24B | SEC24B | 7927 | 0.043 | 0.31 | NO
58 | GNS | GNS | GNS | 8090 | 0.039 | 0.31 | NO
59 | VPS37B | VPS37B | VPS37B | 8182 | 0.037 | 0.3 | NO
60 | AP1G1 | AP1G1 | AP1G1 | 8189 | 0.037 | 0.31 | NO
61 | RAB5C | RAB5C | RAB5C | 8212 | 0.037 | 0.31 | NO
62 | VPS25 | VPS25 | VPS25 | 8266 | 0.035 | 0.31 | NO
63 | CHMP4B | CHMP4B | CHMP4B | 8547 | 0.029 | 0.29 | NO
64 | VAMP2 | VAMP2 | VAMP2 | 8669 | 0.026 | 0.29 | NO
65 | SORT1 | SORT1 | SORT1 | 8737 | 0.025 | 0.29 | NO
66 | VPS37A | VPS37A | VPS37A | 8764 | 0.024 | 0.29 | NO
67 | TSG101 | TSG101 | TSG101 | 8768 | 0.024 | 0.29 | NO
68 | GBF1 | GBF1 | GBF1 | 8789 | 0.024 | 0.29 | NO
69 | HSPA8 | HSPA8 | HSPA8 | 8898 | 0.022 | 0.29 | NO
70 | CHMP4C | CHMP4C | CHMP4C | 8941 | 0.021 | 0.28 | NO
71 | CNO | CNO | CNO | 8946 | 0.021 | 0.29 | NO
72 | AP2M1 | AP2M1 | AP2M1 | 8961 | 0.02 | 0.29 | NO
73 | PICALM | PICALM | PICALM | 9051 | 0.019 | 0.28 | NO
74 | TPD52 | TPD52 | TPD52 | 9143 | 0.017 | 0.28 | NO
75 | SEC31A | SEC31A | SEC31A | 9366 | 0.012 | 0.27 | NO
76 | PREB | PREB | PREB | 9369 | 0.012 | 0.27 | NO
77 | OCRL | OCRL | OCRL | 9589 | 0.0073 | 0.26 | NO
78 | M6PR | M6PR | M6PR | 9904 | 0.00036 | 0.24 | NO
79 | VPS4B | VPS4B | VPS4B | 9913 | 0.00023 | 0.24 | NO
80 | CLTC | CLTC | CLTC | 9965 | -0.0008 | 0.24 | NO
81 | AP4E1 | AP4E1 | AP4E1 | 10045 | -0.0026 | 0.23 | NO
82 | FTH1 | FTH1 | FTH1 | 10107 | -0.004 | 0.23 | NO
83 | ARFGAP1 | ARFGAP1 | ARFGAP1 | 10167 | -0.0055 | 0.23 | NO
84 | TJP1 | TJP1 | TJP1 | 10351 | -0.0092 | 0.22 | NO
85 | VAMP7 | VAMP7 | VAMP7 | 10754 | -0.018 | 0.2 | NO
86 | VPS37C | VPS37C | VPS37C | 10872 | -0.021 | 0.19 | NO
87 | ARF1 | ARF1 | ARF1 | 10874 | -0.021 | 0.19 | NO
88 | PLDN | PLDN | PLDN | 10880 | -0.021 | 0.19 | NO
89 | VAMP8 | VAMP8 | VAMP8 | 11233 | -0.028 | 0.18 | NO
90 | CHMP6 | CHMP6 | CHMP6 | 11301 | -0.03 | 0.18 | NO
91 | SNX2 | SNX2 | SNX2 | 11457 | -0.033 | 0.17 | NO
92 | DNAJC6 | DNAJC6 | DNAJC6 | 11578 | -0.036 | 0.16 | NO
93 | HGS | HGS | HGS | 11588 | -0.036 | 0.17 | NO
94 | SNF8 | SNF8 | SNF8 | 11619 | -0.037 | 0.17 | NO
95 | TXNDC5 | TXNDC5 | TXNDC5 | 11670 | -0.038 | 0.17 | NO
96 | NAPA | NAPA | NAPA | 11733 | -0.039 | 0.17 | NO
97 | CHMP4A | CHMP4A | CHMP4A | 11751 | -0.04 | 0.17 | NO
98 | COPA | COPA | COPA | 11759 | -0.04 | 0.17 | NO
99 | CLTB | CLTB | CLTB | 11785 | -0.041 | 0.17 | NO
100 | TGOLN2 | TGOLN2 | TGOLN2 | 11814 | -0.041 | 0.18 | NO
101 | COPE | COPE | COPE | 12019 | -0.045 | 0.17 | NO
102 | CHMP2A | CHMP2A | CHMP2A | 12049 | -0.046 | 0.17 | NO
103 | SNX5 | SNX5 | SNX5 | 12244 | -0.05 | 0.16 | NO
104 | STX4 | STX4 | STX4 | 12338 | -0.052 | 0.16 | NO
105 | DTNBP1 | DTNBP1 | DTNBP1 | 12401 | -0.054 | 0.16 | NO
106 | BLOC1S1 | BLOC1S1 | BLOC1S1 | 12441 | -0.054 | 0.16 | NO
107 | SEC24C | SEC24C | SEC24C | 12549 | -0.057 | 0.16 | NO
108 | CLTA | CLTA | CLTA | 12652 | -0.06 | 0.16 | NO
109 | STAM | STAM | STAM | 12672 | -0.06 | 0.16 | NO
110 | AP3B1 | AP3B1 | AP3B1 | 12891 | -0.065 | 0.16 | NO
111 | CHMP7 | CHMP7 | CHMP7 | 13641 | -0.086 | 0.12 | NO
112 | BLOC1S3 | BLOC1S3 | BLOC1S3 | 13876 | -0.093 | 0.11 | NO
113 | RPS27A | RPS27A | RPS27A | 13992 | -0.096 | 0.12 | NO
114 | DNASE2 | DNASE2 | DNASE2 | 14110 | -0.1 | 0.12 | NO
115 | COPZ1 | COPZ1 | COPZ1 | 14274 | -0.11 | 0.12 | NO
116 | VPS28 | VPS28 | VPS28 | 14277 | -0.11 | 0.12 | NO
117 | UBA52 | UBA52 | UBA52 | 14355 | -0.11 | 0.13 | NO
118 | DAB2 | DAB2 | DAB2 | 14480 | -0.11 | 0.13 | NO
119 | SNAPIN | SNAPIN | SNAPIN | 14555 | -0.12 | 0.13 | NO
120 | AP1M1 | AP1M1 | AP1M1 | 15500 | -0.16 | 0.092 | NO
121 | GJB1 | GJB1 | GJB1 | 15832 | -0.18 | 0.087 | NO
122 | DNM1 | DNM1 | DNM1 | 16472 | -0.24 | 0.069 | NO
123 | HIP1R | HIP1R | HIP1R | 16896 | -0.3 | 0.068 | NO

Figure S7. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA GPCR PATHWAY.

Figure S8. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA GPCR PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID ER NONGENOMIC PATHWAY

Table S5. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | HERC3 | HERC3 | HERC3 | 575 | 0.53 | 0.011 | YES
2 | FBXO2 | FBXO2 | FBXO2 | 1042 | 0.42 | 0.019 | YES
3 | MID1 | MID1 | MID1 | 1306 | 0.37 | 0.035 | YES
4 | PARK2 | PARK2 | PARK2 | 1807 | 0.31 | 0.032 | YES
5 | DET1 | DET1 | DET1 | 2147 | 0.28 | 0.036 | YES
6 | SOCS3 | SOCS3 | SOCS3 | 2370 | 0.26 | 0.044 | YES
7 | UBE2E2 | UBE2E2 | UBE2E2 | 2670 | 0.24 | 0.047 | YES
8 | SKP2 | SKP2 | SKP2 | 2939 | 0.22 | 0.049 | YES
9 | UBE2C | UBE2C | UBE2C | 3012 | 0.21 | 0.063 | YES
10 | UBE4B | UBE4B | UBE4B | 3187 | 0.2 | 0.069 | YES
11 | CDC26 | CDC26 | CDC26 | 3254 | 0.2 | 0.082 | YES
12 | TRAF6 | TRAF6 | TRAF6 | 3322 | 0.2 | 0.094 | YES
13 | UBE2S | UBE2S | UBE2S | 3427 | 0.19 | 0.1 | YES
14 | CDC20 | CDC20 | CDC20 | 3555 | 0.18 | 0.11 | YES
15 | ANAPC10 | ANAPC10 | ANAPC10 | 3586 | 0.18 | 0.12 | YES
16 | SOCS1 | SOCS1 | SOCS1 | 3636 | 0.18 | 0.14 | YES
17 | UBE2E1 | UBE2E1 | UBE2E1 | 3783 | 0.17 | 0.14 | YES
18 | VHL | VHL | VHL | 4131 | 0.16 | 0.14 | YES
19 | SMURF2 | SMURF2 | SMURF2 | 4140 | 0.16 | 0.15 | YES
20 | FBXW7 | FBXW7 | FBXW7 | 4392 | 0.15 | 0.15 | YES
21 | UBE2O | UBE2O | UBE2O | 4484 | 0.14 | 0.15 | YES
22 | UBE2J1 | UBE2J1 | UBE2J1 | 4625 | 0.14 | 0.16 | YES
23 | BRCA1 | BRCA1 | BRCA1 | 4744 | 0.13 | 0.16 | YES
24 | FANCL | FANCL | FANCL | 4752 | 0.13 | 0.17 | YES
25 | SIAH1 | SIAH1 | SIAH1 | 4761 | 0.13 | 0.18 | YES
26 | CBLB | CBLB | CBLB | 4810 | 0.13 | 0.19 | YES
27 | KLHL13 | KLHL13 | KLHL13 | 4834 | 0.13 | 0.2 | YES
28 | CUL4A | CUL4A | CUL4A | 4916 | 0.13 | 0.2 | YES
29 | CDC27 | CDC27 | CDC27 | 4934 | 0.13 | 0.21 | YES
30 | UBE2H | UBE2H | UBE2H | 5193 | 0.12 | 0.21 | YES
31 | UBA3 | UBA3 | UBA3 | 5260 | 0.12 | 0.21 | YES
32 | BTRC | BTRC | BTRC | 5631 | 0.1 | 0.2 | YES
33 | CUL1 | CUL1 | CUL1 | 5849 | 0.099 | 0.2 | YES
34 | UBE2D4 | UBE2D4 | UBE2D4 | 6129 | 0.09 | 0.19 | YES
35 | UBE2F | UBE2F | UBE2F | 6206 | 0.088 | 0.19 | YES
36 | CDC16 | CDC16 | CDC16 | 6223 | 0.087 | 0.2 | YES
37 | PIAS3 | PIAS3 | PIAS3 | 6227 | 0.087 | 0.21 | YES
38 | UBE2D1 | UBE2D1 | UBE2D1 | 6243 | 0.087 | 0.21 | YES
39 | UBE2K | UBE2K | UBE2K | 6638 | 0.076 | 0.2 | YES
40 | ITCH | ITCH | ITCH | 6868 | 0.07 | 0.19 | YES
41 | ANAPC13 | ANAPC13 | ANAPC13 | 6875 | 0.07 | 0.19 | YES
42 | UBE3C | UBE3C | UBE3C | 6890 | 0.069 | 0.2 | YES
43 | XIAP | XIAP | XIAP | 6930 | 0.068 | 0.2 | YES
44 | PML | PML | PML | 6950 | 0.068 | 0.21 | YES
45 | TRIM32 | TRIM32 | TRIM32 | 7010 | 0.066 | 0.21 | YES
46 | UBE2D3 | UBE2D3 | UBE2D3 | 7063 | 0.065 | 0.21 | YES
47 | ANAPC11 | ANAPC11 | ANAPC11 | 7092 | 0.064 | 0.22 | YES
48 | HERC2 | HERC2 | HERC2 | 7093 | 0.064 | 0.22 | YES
49 | UBR5 | UBR5 | UBR5 | 7136 | 0.063 | 0.22 | YES
50 | UBA1 | UBA1 | UBA1 | 7175 | 0.062 | 0.23 | YES
51 | UBE2N | UBE2N | UBE2N | 7184 | 0.062 | 0.23 | YES
52 | UBA7 | UBA7 | UBA7 | 7221 | 0.061 | 0.23 | YES
53 | BIRC2 | BIRC2 | BIRC2 | 7240 | 0.06 | 0.24 | YES
54 | MDM2 | MDM2 | MDM2 | 7301 | 0.059 | 0.24 | YES
55 | UBE2J2 | UBE2J2 | UBE2J2 | 7336 | 0.058 | 0.24 | YES
56 | BIRC6 | BIRC6 | BIRC6 | 7370 | 0.057 | 0.24 | YES
57 | RHOBTB2 | RHOBTB2 | RHOBTB2 | 7376 | 0.057 | 0.25 | YES
58 | UBE2E3 | UBE2E3 | UBE2E3 | 7388 | 0.057 | 0.25 | YES
59 | RNF7 | RNF7 | RNF7 | 7398 | 0.057 | 0.26 | YES
60 | TRIM37 | TRIM37 | TRIM37 | 7816 | 0.046 | 0.24 | NO
61 | UBE4A | UBE4A | UBE4A | 7908 | 0.044 | 0.24 | NO
62 | UBA6 | UBA6 | UBA6 | 8066 | 0.04 | 0.23 | NO
63 | CBL | CBL | CBL | 8184 | 0.037 | 0.23 | NO
64 | TCEB1 | TCEB1 | TCEB1 | 8260 | 0.035 | 0.22 | NO
65 | KEAP1 | KEAP1 | KEAP1 | 8267 | 0.035 | 0.23 | NO
66 | PIAS1 | PIAS1 | PIAS1 | 8334 | 0.034 | 0.23 | NO
67 | STUB1 | STUB1 | STUB1 | 8353 | 0.033 | 0.23 | NO
68 | SMURF1 | SMURF1 | SMURF1 | 8459 | 0.031 | 0.22 | NO
69 | UBE2G1 | UBE2G1 | UBE2G1 | 8555 | 0.029 | 0.22 | NO
70 | UBE2A | UBE2A | UBE2A | 8653 | 0.027 | 0.22 | NO
71 | TRIP12 | TRIP12 | TRIP12 | 8739 | 0.025 | 0.22 | NO
72 | UBE2W | UBE2W | UBE2W | 9001 | 0.02 | 0.2 | NO
73 | TCEB2 | TCEB2 | TCEB2 | 9005 | 0.02 | 0.2 | NO
74 | WWP2 | WWP2 | WWP2 | 9118 | 0.017 | 0.2 | NO
75 | CUL3 | CUL3 | CUL3 | 9225 | 0.015 | 0.2 | NO
76 | UBA2 | UBA2 | UBA2 | 9238 | 0.015 | 0.2 | NO
77 | CUL4B | CUL4B | CUL4B | 9384 | 0.012 | 0.19 | NO
78 | RBX1 | RBX1 | RBX1 | 9388 | 0.012 | 0.19 | NO
79 | UBE2R2 | UBE2R2 | UBE2R2 | 9407 | 0.011 | 0.19 | NO
80 | SAE1 | SAE1 | SAE1 | 9438 | 0.01 | 0.19 | NO
81 | HERC4 | HERC4 | HERC4 | 9488 | 0.0095 | 0.19 | NO
82 | UBE2NL | UBE2NL | UBE2NL | 9511 | 0.009 | 0.19 | NO
83 | HUWE1 | HUWE1 | HUWE1 | 9517 | 0.0089 | 0.19 | NO
84 | KLHL9 | KLHL9 | KLHL9 | 9574 | 0.0077 | 0.18 | NO
85 | FZR1 | FZR1 | FZR1 | 9579 | 0.0076 | 0.18 | NO
86 | UBE2I | UBE2I | UBE2I | 9590 | 0.0073 | 0.18 | NO
87 | PRPF19 | PRPF19 | PRPF19 | 9618 | 0.0067 | 0.18 | NO
88 | UBE2L3 | UBE2L3 | UBE2L3 | 9654 | 0.0059 | 0.18 | NO
89 | FBXO4 | FBXO4 | FBXO4 | 9793 | 0.0026 | 0.18 | NO
90 | CUL2 | CUL2 | CUL2 | 9879 | 0.00083 | 0.17 | NO
91 | HERC1 | HERC1 | HERC1 | 10056 | -0.0028 | 0.16 | NO
92 | MGRN1 | MGRN1 | MGRN1 | 10136 | -0.0047 | 0.16 | NO
93 | RCHY1 | RCHY1 | RCHY1 | 10240 | -0.0071 | 0.15 | NO
94 | ANAPC7 | ANAPC7 | ANAPC7 | 10264 | -0.0078 | 0.15 | NO
95 | CUL5 | CUL5 | CUL5 | 10285 | -0.0081 | 0.15 | NO
96 | ANAPC1 | ANAPC1 | ANAPC1 | 10350 | -0.0092 | 0.15 | NO
97 | CBLC | CBLC | CBLC | 10396 | -0.01 | 0.15 | NO
98 | UBOX5 | UBOX5 | UBOX5 | 10450 | -0.011 | 0.14 | NO
99 | UBE2QL1 | UBE2QL1 | UBE2QL1 | 10749 | -0.018 | 0.13 | NO
100 | UBE3A | UBE3A | UBE3A | 10801 | -0.019 | 0.13 | NO
101 | ANAPC2 | ANAPC2 | ANAPC2 | 10952 | -0.022 | 0.12 | NO
102 | SKP1 | SKP1 | SKP1 | 11022 | -0.024 | 0.12 | NO
103 | UBE2D2 | UBE2D2 | UBE2D2 | 11058 | -0.024 | 0.12 | NO
104 | PIAS2 | PIAS2 | PIAS2 | 11156 | -0.026 | 0.12 | NO
105 | CDC34 | CDC34 | CDC34 | 11184 | -0.027 | 0.12 | NO
106 | ANAPC5 | ANAPC5 | ANAPC5 | 11374 | -0.031 | 0.11 | NO
107 | UBE2G2 | UBE2G2 | UBE2G2 | 11434 | -0.033 | 0.11 | NO
108 | NHLRC1 | NHLRC1 | NHLRC1 | 11562 | -0.036 | 0.1 | NO
109 | PPIL2 | PPIL2 | PPIL2 | 11596 | -0.036 | 0.1 | NO
110 | UBE3B | UBE3B | UBE3B | 11646 | -0.038 | 0.1 | NO
111 | DDB1 | DDB1 | DDB1 | 11743 | -0.04 | 0.1 | NO
112 | NEDD4L | NEDD4L | NEDD4L | 11767 | -0.04 | 0.1 | NO
113 | FBXW8 | FBXW8 | FBXW8 | 11833 | -0.042 | 0.1 | NO
114 | UBE2Q2 | UBE2Q2 | UBE2Q2 | 12145 | -0.048 | 0.091 | NO
115 | UBE2Z | UBE2Z | UBE2Z | 12714 | -0.061 | 0.064 | NO
116 | UBE2B | UBE2B | UBE2B | 12735 | -0.062 | 0.068 | NO
117 | CDC23 | CDC23 | CDC23 | 12750 | -0.062 | 0.072 | NO
118 | UBE2M | UBE2M | UBE2M | 13236 | -0.074 | 0.051 | NO
119 | ANAPC4 | ANAPC4 | ANAPC4 | 13384 | -0.078 | 0.05 | NO
120 | SYVN1 | SYVN1 | SYVN1 | 13555 | -0.083 | 0.047 | NO
121 | WWP1 | WWP1 | WWP1 | 13620 | -0.085 | 0.05 | NO
122 | CUL7 | CUL7 | CUL7 | 13911 | -0.094 | 0.042 | NO
123 | UBE2Q1 | UBE2Q1 | UBE2Q1 | 14381 | -0.11 | 0.024 | NO
124 | PIAS4 | PIAS4 | PIAS4 | 14444 | -0.11 | 0.03 | NO
125 | RFWD2 | RFWD2 | RFWD2 | 14858 | -0.13 | 0.017 | NO
126 | AIRE | AIRE | AIRE | 15167 | -0.14 | 0.012 | NO
127 | UBE2L6 | UBE2L6 | UBE2L6 | 15244 | -0.15 | 0.019 | NO
128 | BIRC3 | BIRC3 | BIRC3 | 15833 | -0.18 | 0.0013 | NO
129 | FBXW11 | FBXW11 | FBXW11 | 15944 | -0.19 | 0.011 | NO
130 | NEDD4 | NEDD4 | NEDD4 | 15986 | -0.2 | 0.024 | NO
131 | ERCC8 | ERCC8 | ERCC8 | 16006 | -0.2 | 0.039 | NO
132 | DDB2 | DDB2 | DDB2 | 16305 | -0.22 | 0.041 | NO
133 | MAP3K1 | MAP3K1 | MAP3K1 | 16464 | -0.24 | 0.051 | NO
134 | UBE2U | UBE2U | UBE2U | 17718 | -0.5 | 0.022 | NO

Figure S9. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID ER NONGENOMIC PATHWAY.

Figure S10. Get High-res Image For the top 5 core enriched genes in the pathway: PID ER NONGENOMIC PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID MET PATHWAY

Table S6. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | F2RL2 | F2RL2 | F2RL2 | 321 | 0.64 | 0.061 | YES
2 | ARHGEF4 | ARHGEF4 | ARHGEF4 | 741 | 0.48 | 0.097 | YES
3 | RIN2 | RIN2 | RIN2 | 1738 | 0.32 | 0.082 | YES
4 | MAPK8 | MAPK8 | MAPK8 | 2291 | 0.27 | 0.084 | YES
5 | CTNNB1 | CTNNB1 | CTNNB1 | 2340 | 0.26 | 0.11 | YES
6 | SH3KBP1 | SH3KBP1 | SH3KBP1 | 2909 | 0.22 | 0.11 | YES
7 | PARD6A | PARD6A | PARD6A | 2970 | 0.22 | 0.13 | YES
8 | PRKCI | PRKCI | PRKCI | 3304 | 0.2 | 0.14 | YES
9 | MAPK3 | MAPK3 | MAPK3 | 3551 | 0.18 | 0.15 | YES
10 | EIF4E | EIF4E | EIF4E | 3865 | 0.17 | 0.15 | YES
11 | SH3GL2 | SH3GL2 | SH3GL2 | 3869 | 0.17 | 0.17 | YES
12 | SNAI1 | SNAI1 | SNAI1 | 3928 | 0.17 | 0.19 | YES
13 | ETS1 | ETS1 | ETS1 | 3935 | 0.17 | 0.21 | YES
14 | RAB5A | RAB5A | RAB5A | 3947 | 0.17 | 0.23 | YES
15 | PIK3CA | PIK3CA | PIK3CA | 4081 | 0.16 | 0.24 | YES
16 | RAP1B | RAP1B | RAP1B | 4207 | 0.16 | 0.25 | YES
17 | CDC42 | CDC42 | CDC42 | 4354 | 0.15 | 0.26 | YES
18 | RAF1 | RAF1 | RAF1 | 4565 | 0.14 | 0.27 | YES
19 | MTOR | MTOR | MTOR | 4573 | 0.14 | 0.29 | YES
20 | AKT1 | AKT1 | AKT1 | 4692 | 0.14 | 0.3 | YES
21 | RAP1A | RAP1A | RAP1A | 4786 | 0.13 | 0.31 | YES
22 | PAK1 | PAK1 | PAK1 | 4897 | 0.13 | 0.32 | YES
23 | NUMB | NUMB | NUMB | 4945 | 0.13 | 0.33 | YES
24 | PLCG1 | PLCG1 | PLCG1 | 5675 | 0.1 | 0.3 | YES
25 | RHOA | RHOA | RHOA | 5729 | 0.1 | 0.31 | YES
26 | MET | MET | MET | 6214 | 0.087 | 0.3 | YES
27 | PTPN1 | PTPN1 | PTPN1 | 6490 | 0.08 | 0.29 | YES
28 | PTK2 | PTK2 | PTK2 | 6541 | 0.079 | 0.3 | YES
29 | RANBP9 | RANBP9 | RANBP9 | 6575 | 0.078 | 0.31 | YES
30 | PRKCZ | PRKCZ | PRKCZ | 6582 | 0.078 | 0.32 | YES
31 | PAK2 | PAK2 | PAK2 | 6598 | 0.077 | 0.32 | YES
32 | SRC | SRC | SRC | 6743 | 0.073 | 0.32 | YES
33 | HGF | HGF | HGF | 6781 | 0.072 | 0.33 | YES
34 | MAPK1 | MAPK1 | MAPK1 | 6964 | 0.068 | 0.33 | YES
35 | INPP5D | INPP5D | INPP5D | 7007 | 0.067 | 0.34 | YES
36 | JUN | JUN | JUN | 7076 | 0.065 | 0.34 | YES
37 | PXN | PXN | PXN | 7374 | 0.057 | 0.33 | NO
38 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 7452 | 0.055 | 0.33 | NO
39 | NCK1 | NCK1 | NCK1 | 7511 | 0.054 | 0.34 | NO
40 | SOS1 | SOS1 | SOS1 | 7686 | 0.049 | 0.33 | NO
41 | CRK | CRK | CRK | 7731 | 0.048 | 0.34 | NO
42 | HRAS | HRAS | HRAS | 8060 | 0.04 | 0.32 | NO
43 | CBL | CBL | CBL | 8184 | 0.037 | 0.32 | NO
44 | ARF6 | ARF6 | ARF6 | 8218 | 0.036 | 0.32 | NO
45 | INPPL1 | INPPL1 | INPPL1 | 8273 | 0.035 | 0.32 | NO
46 | CRKL | CRKL | CRKL | 8488 | 0.03 | 0.32 | NO
47 | RAC1 | RAC1 | RAC1 | 8686 | 0.026 | 0.31 | NO
48 | EPS15 | EPS15 | EPS15 | 8945 | 0.021 | 0.3 | NO
49 | WASL | WASL | WASL | 9008 | 0.02 | 0.3 | NO
50 | BCAR1 | BCAR1 | BCAR1 | 9065 | 0.018 | 0.3 | NO
51 | MAP2K4 | MAP2K4 | MAP2K4 | 9204 | 0.015 | 0.29 | NO
52 | KPNB1 | KPNB1 | KPNB1 | 9214 | 0.015 | 0.29 | NO
53 | EIF4EBP1 | EIF4EBP1 | EIF4EBP1 | 9220 | 0.015 | 0.29 | NO
54 | MAP2K1 | MAP2K1 | MAP2K1 | 9340 | 0.013 | 0.29 | NO
55 | PDPK1 | PDPK1 | PDPK1 | 9529 | 0.0087 | 0.28 | NO
56 | GRB2 | GRB2 | GRB2 | 9753 | 0.0037 | 0.27 | NO
57 | PTPRJ | PTPRJ | PTPRJ | 10087 | -0.0035 | 0.25 | NO
58 | CTNNA1 | CTNNA1 | CTNNA1 | 10508 | -0.012 | 0.23 | NO
59 | PIK3R1 | PIK3R1 | PIK3R1 | 11051 | -0.024 | 0.2 | NO
60 | MLST8 | MLST8 | MLST8 | 11075 | -0.025 | 0.2 | NO
61 | GAB1 | GAB1 | GAB1 | 11391 | -0.032 | 0.19 | NO
62 | HGS | HGS | HGS | 11588 | -0.036 | 0.18 | NO
63 | RPTOR | RPTOR | RPTOR | 11636 | -0.037 | 0.18 | NO
64 | PTPN11 | PTPN11 | PTPN11 | 11821 | -0.041 | 0.18 | NO
65 | RANBP10 | RANBP10 | RANBP10 | 11927 | -0.043 | 0.18 | NO
66 | CDH1 | CDH1 | CDH1 | 12179 | -0.049 | 0.17 | NO
67 | MAP2K2 | MAP2K2 | MAP2K2 | 12248 | -0.05 | 0.17 | NO
68 | MUC20 | MUC20 | MUC20 | 12277 | -0.051 | 0.18 | NO
69 | BAD | BAD | BAD | 12816 | -0.063 | 0.16 | NO
70 | EGR1 | EGR1 | EGR1 | 12915 | -0.066 | 0.16 | NO
71 | PAK4 | PAK4 | PAK4 | 13036 | -0.068 | 0.16 | NO
72 | SHC1 | SHC1 | SHC1 | 13047 | -0.069 | 0.17 | NO
73 | NCK2 | NCK2 | NCK2 | 13186 | -0.072 | 0.17 | NO
74 | GAB2 | GAB2 | GAB2 | 13627 | -0.085 | 0.16 | NO
75 | APC | APC | APC | 13927 | -0.094 | 0.15 | NO
76 | AKT1S1 | AKT1S1 | AKT1S1 | 14362 | -0.11 | 0.14 | NO
77 | AKT2 | AKT2 | AKT2 | 14805 | -0.13 | 0.13 | NO
78 | PTPN2 | PTPN2 | PTPN2 | 15901 | -0.19 | 0.093 | NO
79 | MAP3K1 | MAP3K1 | MAP3K1 | 16464 | -0.24 | 0.091 | NO

Figure S11. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID MET PATHWAY.

Figure S12. Get High-res Image For the top 5 core enriched genes in the pathway: PID MET PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID CDC42 PATHWAY

Table S7. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | AGPAT9 | AGPAT9 | AGPAT9 | 25 | 0.98 | 0.16 | YES
2 | PLA2G10 | PLA2G10 | PLA2G10 | 170 | 0.73 | 0.26 | YES
3 | PLA2G4A | PLA2G4A | PLA2G4A | 450 | 0.57 | 0.34 | YES
4 | PLA2G2F | PLA2G2F | PLA2G2F | 637 | 0.51 | 0.41 | YES
5 | PLA2G1B | PLA2G1B | PLA2G1B | 1136 | 0.4 | 0.45 | YES
6 | GPD1L | GPD1L | GPD1L | 1151 | 0.4 | 0.51 | YES
7 | GPAT2 | GPAT2 | GPAT2 | 1432 | 0.36 | 0.55 | YES
8 | AGPAT4 | AGPAT4 | AGPAT4 | 1956 | 0.3 | 0.57 | YES
9 | PLA2G4D | PLA2G4D | PLA2G4D | 2823 | 0.22 | 0.56 | NO
10 | LCLAT1 | LCLAT1 | LCLAT1 | 3490 | 0.19 | 0.55 | NO
11 | PLA2G5 | PLA2G5 | PLA2G5 | 5174 | 0.12 | 0.48 | NO
12 | LPCAT4 | LPCAT4 | LPCAT4 | 7478 | 0.055 | 0.36 | NO
13 | AGPAT5 | AGPAT5 | AGPAT5 | 8168 | 0.038 | 0.32 | NO
14 | LPCAT1 | LPCAT1 | LPCAT1 | 9466 | 0.01 | 0.25 | NO
15 | PLA2G12A | PLA2G12A | PLA2G12A | 10739 | -0.017 | 0.19 | NO
16 | AGPAT2 | AGPAT2 | AGPAT2 | 11792 | -0.041 | 0.14 | NO
17 | GPAM | GPAM | GPAM | 11926 | -0.043 | 0.13 | NO
18 | PLD2 | PLD2 | PLD2 | 12108 | -0.047 | 0.13 | NO
19 | PLA2G2D | PLA2G2D | PLA2G2D | 12835 | -0.064 | 0.1 | NO
20 | AGPAT1 | AGPAT1 | AGPAT1 | 12863 | -0.064 | 0.11 | NO
21 | AGPAT3 | AGPAT3 | AGPAT3 | 13246 | -0.075 | 0.1 | NO
22 | GPD1 | GPD1 | GPD1 | 13494 | -0.081 | 0.1 | NO
23 | GNPAT | GNPAT | GNPAT | 14267 | -0.11 | 0.075 | NO
24 | AGPAT6 | AGPAT6 | AGPAT6 | 15414 | -0.16 | 0.036 | NO
25 | PLD1 | PLD1 | PLD1 | 16792 | -0.28 | 0.0048 | NO
26 | PLA2G2A | PLA2G2A | PLA2G2A | 17504 | -0.43 | 0.034 | NO

Figure S13. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID CDC42 PATHWAY.

Figure S14. Get High-res Image For the top 5 core enriched genes in the pathway: PID CDC42 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID RETINOIC ACID PATHWAY

Table S8. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | MAP3K5 | MAP3K5 | MAP3K5 | 1077 | 0.41 | 0.042 | YES
2 | FOXO1 | FOXO1 | FOXO1 | 2499 | 0.25 | 0.024 | YES
3 | SFN | SFN | SFN | 2657 | 0.24 | 0.073 | YES
4 | TBC1D4 | TBC1D4 | TBC1D4 | 2804 | 0.23 | 0.12 | YES
5 | CASP9 | CASP9 | CASP9 | 2816 | 0.22 | 0.18 | YES
6 | FOXO3 | FOXO3 | FOXO3 | 2952 | 0.22 | 0.22 | YES
7 | SLC2A4 | SLC2A4 | SLC2A4 | 4383 | 0.15 | 0.18 | YES
8 | RAF1 | RAF1 | RAF1 | 4565 | 0.14 | 0.2 | YES
9 | MTOR | MTOR | MTOR | 4573 | 0.14 | 0.24 | YES
10 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 4605 | 0.14 | 0.27 | YES
11 | AKT1 | AKT1 | AKT1 | 4692 | 0.14 | 0.3 | YES
12 | CDKN1B | CDKN1B | CDKN1B | 4893 | 0.13 | 0.32 | YES
13 | KPNA1 | KPNA1 | KPNA1 | 5536 | 0.11 | 0.31 | YES
14 | FOXO4 | FOXO4 | FOXO4 | 5799 | 0.1 | 0.32 | YES
15 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 6285 | 0.086 | 0.31 | YES
16 | YWHAZ | YWHAZ | YWHAZ | 6493 | 0.08 | 0.32 | YES
17 | SRC | SRC | SRC | 6743 | 0.073 | 0.32 | YES
18 | CHUK | CHUK | CHUK | 6773 | 0.072 | 0.34 | YES
19 | PRKDC | PRKDC | PRKDC | 6817 | 0.071 | 0.36 | YES
20 | GSK3B | GSK3B | GSK3B | 6992 | 0.067 | 0.36 | YES
21 | YWHAB | YWHAB | YWHAB | 7116 | 0.064 | 0.37 | YES
22 | YWHAG | YWHAG | YWHAG | 7697 | 0.049 | 0.35 | NO
23 | YWHAE | YWHAE | YWHAE | 8321 | 0.034 | 0.32 | NO
24 | PDPK1 | PDPK1 | PDPK1 | 9529 | 0.0087 | 0.26 | NO
25 | PRKACA | PRKACA | PRKACA | 10370 | -0.0095 | 0.22 | NO
26 | CDKN1A | CDKN1A | CDKN1A | 10916 | -0.022 | 0.19 | NO
27 | MLST8 | MLST8 | MLST8 | 11075 | -0.025 | 0.19 | NO
28 | YWHAQ | YWHAQ | YWHAQ | 11610 | -0.037 | 0.17 | NO
29 | YWHAH | YWHAH | YWHAH | 12075 | -0.046 | 0.15 | NO
30 | GSK3A | GSK3A | GSK3A | 12182 | -0.049 | 0.16 | NO
31 | BAD | BAD | BAD | 12816 | -0.063 | 0.14 | NO
32 | RICTOR | RICTOR | RICTOR | 13242 | -0.075 | 0.14 | NO
33 | AKT2 | AKT2 | AKT2 | 14805 | -0.13 | 0.08 | NO
34 | AKT3 | AKT3 | AKT3 | 16090 | -0.21 | 0.059 | NO
35 | BCL2L1 | BCL2L1 | BCL2L1 | 16219 | -0.22 | 0.1 | NO

Figure S15. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID RETINOIC ACID PATHWAY.

Figure S16. Get High-res Image For the top 5 core enriched genes in the pathway: PID RETINOIC ACID PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID DELTANP63PATHWAY

Table S9. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | GRIA1 | GRIA1 | GRIA1 | 709 | 0.49 | 0.096 | YES
2 | GRIA2 | GRIA2 | GRIA2 | 713 | 0.49 | 0.23 | YES
3 | GRIA3 | GRIA3 | GRIA3 | 938 | 0.44 | 0.34 | YES
4 | PRKCG | PRKCG | PRKCG | 1032 | 0.42 | 0.45 | YES
5 | CACNG4 | CACNG4 | CACNG4 | 1159 | 0.4 | 0.56 | YES
6 | AKAP5 | AKAP5 | AKAP5 | 3390 | 0.19 | 0.49 | NO
7 | NSF | NSF | NSF | 5704 | 0.1 | 0.39 | NO
8 | MYO6 | MYO6 | MYO6 | 5772 | 0.1 | 0.41 | NO
9 | CAMK2D | CAMK2D | CAMK2D | 5931 | 0.096 | 0.43 | NO
10 | DLG1 | DLG1 | DLG1 | 5993 | 0.094 | 0.45 | NO
11 | PRKCA | PRKCA | PRKCA | 6132 | 0.09 | 0.47 | NO
12 | CACNG3 | CACNG3 | CACNG3 | 6966 | 0.068 | 0.44 | NO
13 | MDM2 | MDM2 | MDM2 | 7301 | 0.059 | 0.44 | NO
14 | AP2S1 | AP2S1 | AP2S1 | 8027 | 0.041 | 0.41 | NO
15 | AP2A1 | AP2A1 | AP2A1 | 8604 | 0.028 | 0.39 | NO
16 | AP2M1 | AP2M1 | AP2M1 | 8961 | 0.02 | 0.37 | NO
17 | CAMK2B | CAMK2B | CAMK2B | 10717 | -0.017 | 0.28 | NO
18 | PRKCB | PRKCB | PRKCB | 11448 | -0.033 | 0.25 | NO
19 | AP2B1 | AP2B1 | AP2B1 | 11663 | -0.038 | 0.25 | NO
20 | EPB41L1 | EPB41L1 | EPB41L1 | 12028 | -0.045 | 0.24 | NO
21 | AP2A2 | AP2A2 | AP2A2 | 12043 | -0.046 | 0.25 | NO
22 | GRIA4 | GRIA4 | GRIA4 | 12135 | -0.048 | 0.26 | NO
23 | CAMK2A | CAMK2A | CAMK2A | 13009 | -0.068 | 0.23 | NO
24 | PICK1 | PICK1 | PICK1 | 13865 | -0.092 | 0.21 | NO
25 | GRIP2 | GRIP2 | GRIP2 | 13935 | -0.094 | 0.23 | NO

Figure S17. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID DELTANP63PATHWAY.

Figure S18. Get High-res Image For the top 5 core enriched genes in the pathway: PID DELTANP63PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID A6B1 A6B4 INTEGRIN PATHWAY

Table S10. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | PIP5K1B | PIP5K1B | PIP5K1B | 302 | 0.65 | 0.1 | YES
2 | INPP4B | INPP4B | INPP4B | 522 | 0.55 | 0.19 | YES
3 | TPTE2 | TPTE2 | TPTE2 | 1314 | 0.37 | 0.22 | YES
4 | PIK3C2G | PIK3C2G | PIK3C2G | 1750 | 0.32 | 0.25 | YES
5 | PIK3CG | PIK3CG | PIK3CG | 2550 | 0.24 | 0.26 | YES
6 | PIK3R3 | PIK3R3 | PIK3R3 | 2846 | 0.22 | 0.28 | YES
7 | FIG4 | FIG4 | FIG4 | 2964 | 0.22 | 0.31 | YES
8 | SACM1L | SACM1L | SACM1L | 3377 | 0.19 | 0.33 | YES
9 | MTM1 | MTM1 | MTM1 | 3788 | 0.17 | 0.34 | YES
10 | PIK3CD | PIK3CD | PIK3CD | 3972 | 0.16 | 0.36 | YES
11 | PIK3CA | PIK3CA | PIK3CA | 4081 | 0.16 | 0.38 | YES
12 | PIP4K2A | PIP4K2A | PIP4K2A | 4362 | 0.15 | 0.39 | YES
13 | PIK3R5 | PIK3R5 | PIK3R5 | 5119 | 0.12 | 0.37 | YES
14 | MTMR6 | MTMR6 | MTMR6 | 5137 | 0.12 | 0.4 | YES
15 | PIK3R4 | PIK3R4 | PIK3R4 | 5444 | 0.11 | 0.4 | YES
16 | PIK3C2A | PIK3C2A | PIK3C2A | 5587 | 0.11 | 0.41 | YES
17 | MTMR2 | MTMR2 | MTMR2 | 6040 | 0.093 | 0.4 | YES
18 | PI4K2B | PI4K2B | PI4K2B | 6108 | 0.091 | 0.42 | YES
19 | PI4K2A | PI4K2A | PI4K2A | 6137 | 0.09 | 0.43 | YES
20 | PITPNB | PITPNB | PITPNB | 6587 | 0.078 | 0.42 | NO
21 | PIK3CB | PIK3CB | PIK3CB | 7508 | 0.054 | 0.38 | NO
22 | PTEN | PTEN | PTEN | 7787 | 0.047 | 0.37 | NO
23 | PIP5K1C | PIP5K1C | PIP5K1C | 7928 | 0.043 | 0.37 | NO
24 | VAC14 | VAC14 | VAC14 | 8039 | 0.041 | 0.38 | NO
25 | MTMR3 | MTMR3 | MTMR3 | 8115 | 0.039 | 0.38 | NO
26 | INPPL1 | INPPL1 | INPPL1 | 8273 | 0.035 | 0.38 | NO
27 | SYNJ2 | SYNJ2 | SYNJ2 | 8422 | 0.032 | 0.37 | NO
28 | PIKFYVE | PIKFYVE | PIKFYVE | 8822 | 0.023 | 0.36 | NO
29 | PIK3C2B | PIK3C2B | PIK3C2B | 9468 | 0.01 | 0.32 | NO
30 | OCRL | OCRL | OCRL | 9589 | 0.0073 | 0.32 | NO
31 | INPP5E | INPP5E | INPP5E | 9683 | 0.0052 | 0.31 | NO
32 | PI4KA | PI4KA | PI4KA | 9786 | 0.0027 | 0.31 | NO
33 | PIP4K2B | PIP4K2B | PIP4K2B | 9959 | -0.0007 | 0.3 | NO
34 | MTMR4 | MTMR4 | MTMR4 | 10183 | -0.006 | 0.29 | NO
35 | INPP5K | INPP5K | INPP5K | 10573 | -0.014 | 0.27 | NO
36 | ARF1 | ARF1 | ARF1 | 10874 | -0.021 | 0.26 | NO
37 | PIK3R1 | PIK3R1 | PIK3R1 | 11051 | -0.024 | 0.25 | NO
38 | PIK3C3 | PIK3C3 | PIK3C3 | 11229 | -0.028 | 0.25 | NO
39 | ARF3 | ARF3 | ARF3 | 11871 | -0.042 | 0.22 | NO
40 | MTMR1 | MTMR1 | MTMR1 | 12054 | -0.046 | 0.22 | NO
41 | MTMR14 | MTMR14 | MTMR14 | 12148 | -0.048 | 0.22 | NO
42 | PIK3R2 | PIK3R2 | PIK3R2 | 13077 | -0.07 | 0.18 | NO
43 | SYNJ1 | SYNJ1 | SYNJ1 | 13362 | -0.078 | 0.18 | NO
44 | PI4KB | PI4KB | PI4KB | 13690 | -0.087 | 0.18 | NO
45 | PIK3R6 | PIK3R6 | PIK3R6 | 13948 | -0.095 | 0.18 | NO
46 | MTMR7 | MTMR7 | MTMR7 | 14201 | -0.1 | 0.19 | NO
47 | INPP5J | INPP5J | INPP5J | 15427 | -0.16 | 0.15 | NO

Figure S19. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID A6B1 A6B4 INTEGRIN PATHWAY.

Figure S20. Get High-res Image For the top 5 core enriched genes in the pathway: PID A6B1 A6B4 INTEGRIN PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

For the top enriched genes, if you want to check whether they are

- up-regulated, please check the list of up-regulated genes

- down-regulated, please check the list of down-regulated genes

Expression level

For the top enriched genes, if you want to check whether they are

- highly expressed genes, please check the list of high (top 30%) expressed genes

- low expressed genes, please check the list of low (bottom 30%) expressed genes

An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap

Significant gene list

For the top enriched genes, if you want to check whether they are

- significantly differently expressed genes by eBayes lm fit, please check the list of significant genes

Subtype clus2 enriched pathways

Table 4. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus2. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
KEGG CITRATE CYCLE TCA CYCLE | 29 | genes.ES.table | 0.64 | 1.6 | 0.067 | 0.67 | 0.91 | 0.59 | 0.12 | 0.52 | 0.38 | 0.22
KEGG OXIDATIVE PHOSPHORYLATION | 111 | genes.ES.table | 0.51 | 1.5 | 0.13 | 0.94 | 0.97 | 0.59 | 0.2 | 0.47 | 0.67 | 0.35
KEGG AMINOACYL TRNA BIOSYNTHESIS | 41 | genes.ES.table | 0.44 | 1.8 | 0.037 | 0.63 | 0.6 | 0.51 | 0.29 | 0.36 | 0.2 | 0.17
KEGG ALZHEIMERS DISEASE | 152 | genes.ES.table | 0.33 | 1.4 | 0.084 | 1 | 0.99 | 0.44 | 0.19 | 0.36 | 0.99 | 0.5
KEGG PARKINSONS DISEASE | 110 | genes.ES.table | 0.45 | 1.4 | 0.18 | 1 | 0.99 | 0.55 | 0.19 | 0.45 | 0.92 | 0.46
KEGG HUNTINGTONS DISEASE | 166 | genes.ES.table | 0.36 | 1.6 | 0.056 | 0.68 | 0.94 | 0.48 | 0.22 | 0.38 | 0.42 | 0.23
ST GAQ PATHWAY | 27 | genes.ES.table | 0.48 | 1.7 | 0.027 | 0.75 | 0.75 | 0.41 | 0.21 | 0.32 | 0.3 | 0.22
PID MTOR 4PATHWAY | 67 | genes.ES.table | 0.25 | 1.3 | 0.16 | 1 | 1 | 0.15 | 0.13 | 0.13 | 1 | 0.74
REACTOME TRANSLATION | 146 | genes.ES.table | 0.39 | 1.3 | 0.28 | 1 | 1 | 0.62 | 0.37 | 0.4 | 1 | 0.77
REACTOME PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE | 40 | genes.ES.table | 0.5 | 1.6 | 0.057 | 0.66 | 0.89 | 0.45 | 0.12 | 0.4 | 0.35 | 0.21

genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

Table S11. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | SLC25A4 | SLC25A4 | SLC25A4 | 655 | 0.29 | 0.013 | YES
2 | ATP5G1 | ATP5G1 | ATP5G1 | 752 | 0.27 | 0.054 | YES
3 | FXN | FXN | FXN | 760 | 0.27 | 0.1 | YES
4 | TOMM40 | TOMM40 | TOMM40 | 868 | 0.25 | 0.14 | YES
5 | CS | CS | CS | 996 | 0.24 | 0.17 | YES
6 | ATP5B | ATP5B | ATP5B | 1122 | 0.22 | 0.2 | YES
7 | LDHD | LDHD | LDHD | 1128 | 0.22 | 0.24 | YES
8 | ACO2 | ACO2 | ACO2 | 1149 | 0.22 | 0.28 | YES
9 | DNAJC19 | DNAJC19 | DNAJC19 | 1305 | 0.2 | 0.3 | YES
10 | TIMM50 | TIMM50 | TIMM50 | 1363 | 0.2 | 0.33 | YES
11 | GRPEL1 | GRPEL1 | GRPEL1 | 1464 | 0.19 | 0.36 | YES
12 | CHCHD4 | CHCHD4 | CHCHD4 | 1498 | 0.19 | 0.39 | YES
13 | ATP5A1 | ATP5A1 | ATP5A1 | 1551 | 0.18 | 0.42 | YES
14 | C18orf55 | C18orf55 | C18orf55 | 1884 | 0.16 | 0.43 | YES
15 | TIMM22 | TIMM22 | TIMM22 | 1944 | 0.16 | 0.45 | YES
16 | CYC1 | CYC1 | CYC1 | 2004 | 0.16 | 0.48 | YES
17 | TIMM17A | TIMM17A | TIMM17A | 2032 | 0.16 | 0.5 | YES
18 | TOMM5 | TOMM5 | TOMM5 | 2040 | 0.15 | 0.53 | YES
19 | TIMM10 | TIMM10 | TIMM10 | 2209 | 0.14 | 0.54 | YES
20 | TIMM44 | TIMM44 | TIMM44 | 2354 | 0.14 | 0.56 | YES
21 | MTX1 | MTX1 | MTX1 | 2729 | 0.12 | 0.56 | YES
22 | SAMM50 | SAMM50 | SAMM50 | 2779 | 0.12 | 0.58 | YES
23 | PMPCA | PMPCA | PMPCA | 2834 | 0.12 | 0.59 | YES
24 | MTX2 | MTX2 | MTX2 | 3082 | 0.11 | 0.6 | YES
25 | TIMM13 | TIMM13 | TIMM13 | 3228 | 0.1 | 0.61 | YES
26 | SLC25A6 | SLC25A6 | SLC25A6 | 3483 | 0.095 | 0.61 | YES
27 | TAZ | TAZ | TAZ | 3586 | 0.092 | 0.62 | YES
28 | TOMM20 | TOMM20 | TOMM20 | 3700 | 0.089 | 0.63 | YES
29 | VDAC1 | VDAC1 | VDAC1 | 3725 | 0.088 | 0.64 | YES
30 | TIMM8B | TIMM8B | TIMM8B | 3967 | 0.082 | 0.64 | YES
31 | FXC1 | FXC1 | FXC1 | 4005 | 0.08 | 0.65 | YES
32 | COQ2 | COQ2 | COQ2 | 4012 | 0.08 | 0.67 | YES
33 | HSPA9 | HSPA9 | HSPA9 | 4037 | 0.079 | 0.68 | YES
34 | HSPD1 | HSPD1 | HSPD1 | 4411 | 0.07 | 0.67 | NO
35 | GFER | GFER | GFER | 4625 | 0.064 | 0.67 | NO
36 | IDH3G | IDH3G | IDH3G | 5192 | 0.053 | 0.65 | NO
37 | TOMM22 | TOMM22 | TOMM22 | 5462 | 0.047 | 0.64 | NO
38 | SLC25A12 | SLC25A12 | SLC25A12 | 5751 | 0.041 | 0.63 | NO
39 | TIMM17B | TIMM17B | TIMM17B | 5843 | 0.039 | 0.63 | NO
40 | COX17 | COX17 | COX17 | 5987 | 0.037 | 0.63 | NO
41 | BCS1L | BCS1L | BCS1L | 6350 | 0.03 | 0.62 | NO
42 | PMPCB | PMPCB | PMPCB | 6541 | 0.026 | 0.61 | NO
43 | TOMM70A | TOMM70A | TOMM70A | 7019 | 0.016 | 0.59 | NO
44 | TOMM7 | TOMM7 | TOMM7 | 7394 | 0.0091 | 0.57 | NO
45 | HSCB | HSCB | HSCB | 7606 | 0.0049 | 0.56 | NO
46 | GRPEL2 | GRPEL2 | GRPEL2 | 9098 | -0.024 | 0.48 | NO
47 | TIMM9 | TIMM9 | TIMM9 | 9696 | -0.037 | 0.45 | NO
48 | SLC25A13 | SLC25A13 | SLC25A13 | 9822 | -0.04 | 0.45 | NO
49 | TIMM8A | TIMM8A | TIMM8A | 9878 | -0.041 | 0.46 | NO

Figure S21. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CITRATE CYCLE TCA CYCLE.

Figure S22. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CITRATE CYCLE TCA CYCLE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG OXIDATIVE PHOSPHORYLATION

Table S12. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | ADHFE1 | ADHFE1 | ADHFE1 | 176 | 0.46 | 0.016 | YES
2 | NDUFA8 | NDUFA8 | NDUFA8 | 412 | 0.35 | 0.022 | YES
3 | IDH3A | IDH3A | IDH3A | 415 | 0.35 | 0.041 | YES
4 | NNT | NNT | NNT | 482 | 0.33 | 0.056 | YES
5 | UQCRFS1 | UQCRFS1 | UQCRFS1 | 504 | 0.32 | 0.073 | YES
6 | NDUFB5 | NDUFB5 | NDUFB5 | 634 | 0.29 | 0.082 | YES
7 | COX5A | COX5A | COX5A | 713 | 0.28 | 0.093 | YES
8 | COX7B | COX7B | COX7B | 746 | 0.27 | 0.11 | YES
9 | ATP5G1 | ATP5G1 | ATP5G1 | 752 | 0.27 | 0.12 | YES
10 | COX6B1 | COX6B1 | COX6B1 | 875 | 0.25 | 0.13 | YES
11 | CYCS | CYCS | CYCS | 879 | 0.25 | 0.14 | YES
12 | NDUFA12 | NDUFA12 | NDUFA12 | 926 | 0.25 | 0.15 | YES
13 | ATP5D | ATP5D | ATP5D | 972 | 0.24 | 0.16 | YES
14 | SDHA | SDHA | SDHA | 992 | 0.24 | 0.18 | YES
15 | CS | CS | CS | 996 | 0.24 | 0.19 | YES
16 | PDHA1 | PDHA1 | PDHA1 | 1024 | 0.24 | 0.2 | YES
17 | SUCLG1 | SUCLG1 | SUCLG1 | 1033 | 0.23 | 0.21 | YES
18 | NDUFS4 | NDUFS4 | NDUFS4 | 1091 | 0.23 | 0.22 | YES
19 | NDUFS3 | NDUFS3 | NDUFS3 | 1092 | 0.23 | 0.24 | YES
20 | ATP5B | ATP5B | ATP5B | 1122 | 0.22 | 0.25 | YES
21 | ACO2 | ACO2 | ACO2 | 1149 | 0.22 | 0.26 | YES
22 | COX5B | COX5B | COX5B | 1157 | 0.22 | 0.27 | YES
23 | SUCLA2 | SUCLA2 | SUCLA2 | 1183 | 0.22 | 0.28 | YES
24 | NDUFB6 | NDUFB6 | NDUFB6 | 1217 | 0.22 | 0.29 | YES
25 | ATP5O | ATP5O | ATP5O | 1233 | 0.21 | 0.3 | YES
26 | SDHD | SDHD | SDHD | 1319 | 0.2 | 0.31 | YES
27 | NDUFV3 | NDUFV3 | NDUFV3 | 1337 | 0.2 | 0.32 | YES
28 | OGDH | OGDH | OGDH | 1359 | 0.2 | 0.33 | YES
29 | ATP5J | ATP5J | ATP5J | 1393 | 0.2 | 0.34 | YES
30 | ATP5C1 | ATP5C1 | ATP5C1 | 1394 | 0.2 | 0.35 | YES
31 | UQCRB | UQCRB | UQCRB | 1438 | 0.19 | 0.36 | YES
32 | COX8A | COX8A | COX8A | 1447 | 0.19 | 0.37 | YES
33 | NDUFA6 | NDUFA6 | NDUFA6 | 1523 | 0.19 | 0.37 | YES
34 | ATP5A1 | ATP5A1 | ATP5A1 | 1551 | 0.18 | 0.38 | YES
35 | UQCR11 | UQCR11 | UQCR11 | 1570 | 0.18 | 0.39 | YES
36 | DLAT | DLAT | DLAT | 1579 | 0.18 | 0.4 | YES
37 | IDH2 | IDH2 | IDH2 | 1631 | 0.18 | 0.41 | YES
38 | ATP5L | ATP5L | ATP5L | 1751 | 0.17 | 0.41 | YES
39 | COX7C | COX7C | COX7C | 1780 | 0.17 | 0.42 | YES
40 | FH | FH | FH | 1795 | 0.17 | 0.43 | YES
41 | UQCRC2 | UQCRC2 | UQCRC2 | 1798 | 0.17 | 0.44 | YES
42 | LDHA | LDHA | LDHA | 1839 | 0.17 | 0.44 | YES
43 | COX4I1 | COX4I1 | COX4I1 | 1865 | 0.16 | 0.45 | YES
44 | COX6A1 | COX6A1 | COX6A1 | 1921 | 0.16 | 0.46 | YES
45 | DLD | DLD | DLD | 1922 | 0.16 | 0.47 | YES
46 | NDUFA1 | NDUFA1 | NDUFA1 | 1988 | 0.16 | 0.47 | YES
47 | NDUFA4 | NDUFA4 | NDUFA4 | 1991 | 0.16 | 0.48 | YES
48 | CYC1 | CYC1 | CYC1 | 2004 | 0.16 | 0.49 | YES
49 | NDUFA3 | NDUFA3 | NDUFA3 | 2052 | 0.15 | 0.49 | YES
50 | ATP5J2 | ATP5J2 | ATP5J2 | 2083 | 0.15 | 0.5 | YES
51 | NDUFS7 | NDUFS7 | NDUFS7 | 2100 | 0.15 | 0.51 | YES
52 | NDUFB2 | NDUFB2 | NDUFB2 | 2130 | 0.15 | 0.51 | YES
53 | UQCRC1 | UQCRC1 | UQCRC1 | 2162 | 0.15 | 0.52 | YES
54 | ATP5H | ATP5H | ATP5H | 2171 | 0.15 | 0.53 | YES
55 | MDH2 | MDH2 | MDH2 | 2178 | 0.15 | 0.54 | YES
56 | NDUFA10 | NDUFA10 | NDUFA10 | 2182 | 0.15 | 0.54 | YES
57 | NDUFB3 | NDUFB3 | NDUFB3 | 2202 | 0.15 | 0.55 | YES
58 | ATP5I | ATP5I | ATP5I | 2217 | 0.14 | 0.56 | YES
59 | NDUFB9 | NDUFB9 | NDUFB9 | 2222 | 0.14 | 0.57 | YES
60 | PDHX | PDHX | PDHX | 2247 | 0.14 | 0.57 | YES
61 | NDUFA13 | NDUFA13 | NDUFA13 | 2362 | 0.14 | 0.57 | YES
62 | UQCRQ | UQCRQ | UQCRQ | 2398 | 0.14 | 0.58 | YES
63 | NDUFB7 | NDUFB7 | NDUFB7 | 2479 | 0.13 | 0.58 | YES
64 | SDHC | SDHC | SDHC | 2757 | 0.12 | 0.57 | YES
65 | NDUFB10 | NDUFB10 | NDUFB10 | 2825 | 0.12 | 0.58 | YES
66 | NDUFS8 | NDUFS8 | NDUFS8 | 2826 | 0.12 | 0.58 | YES
67 | NDUFS2 | NDUFS2 | NDUFS2 | 2829 | 0.12 | 0.59 | YES
68 | NDUFS1 | NDUFS1 | NDUFS1 | 2863 | 0.12 | 0.59 | YES
69 | NDUFV2 | NDUFV2 | NDUFV2 | 2974 | 0.11 | 0.59 | YES
70 | COX6C | COX6C | COX6C | 3073 | 0.11 | 0.6 | YES
71 | NDUFAB1 | NDUFAB1 | NDUFAB1 | 3132 | 0.11 | 0.6 | YES
72 | PDPR | PDPR | PDPR | 3273 | 0.1 | 0.6 | YES
73 | SDHB | SDHB | SDHB | 3291 | 0.1 | 0.6 | YES
74 | NDUFA7 | NDUFA7 | NDUFA7 | 3304 | 0.1 | 0.6 | YES
75 | NDUFA9 | NDUFA9 | NDUFA9 | 3360 | 0.1 | 0.61 | YES
76 | DLST | DLST | DLST | 3612 | 0.092 | 0.6 | NO
77 | NDUFV1 | NDUFV1 | NDUFV1 | 3632 | 0.091 | 0.6 | NO
78 | D2HGDH | D2HGDH | D2HGDH | 3688 | 0.089 | 0.6 | NO
79 | ATP5E | ATP5E | ATP5E | 3790 | 0.086 | 0.6 | NO
80 | NDUFC1 | NDUFC1 | NDUFC1 | 3839 | 0.085 | 0.61 | NO
81 | NDUFS6 | NDUFS6 | NDUFS6 | 4088 | 0.078 | 0.6 | NO
82 | ATP5F1 | ATP5F1 | ATP5F1 | 4255 | 0.074 | 0.59 | NO
83 | NDUFA2 | NDUFA2 | NDUFA2 | 4258 | 0.074 | 0.6 | NO
84 | NDUFA11 | NDUFA11 | NDUFA11 | 4271 | 0.074 | 0.6 | NO
85 | NDUFB4 | NDUFB4 | NDUFB4 | 4371 | 0.071 | 0.6 | NO
86 | ETFA | ETFA | ETFA | 4372 | 0.071 | 0.6 | NO
87 | NDUFB1 | NDUFB1 | NDUFB1 | 4788 | 0.061 | 0.58 | NO
88 | IDH3G | IDH3G | IDH3G | 5192 | 0.053 | 0.56 | NO
89 | ETFB | ETFB | ETFB | 5219 | 0.052 | 0.56 | NO
90 | NDUFB8 | NDUFB8 | NDUFB8 | 5220 | 0.052 | 0.57 | NO
91 | BSG | BSG | BSG | 5277 | 0.051 | 0.57 | NO
92 | IDH3B | IDH3B | IDH3B | 5416 | 0.048 | 0.56 | NO
93 | NDUFA5 | NDUFA5 | NDUFA5 | 5714 | 0.042 | 0.55 | NO
94 | COX7A2L | COX7A2L | COX7A2L | 5827 | 0.04 | 0.54 | NO
95 | NDUFS5 | NDUFS5 | NDUFS5 | 6167 | 0.033 | 0.53 | NO
96 | NDUFC2 | NDUFC2 | NDUFC2 | 6181 | 0.033 | 0.53 | NO
97 | PDK2 | PDK2 | PDK2 | 6286 | 0.03 | 0.52 | NO
98 | PDK1 | PDK1 | PDK1 | 6660 | 0.023 | 0.5 | NO
99 | PDHB | PDHB | PDHB | 6768 | 0.021 | 0.5 | NO
100 | UQCRHL | UQCRHL | UQCRHL | 7431 | 0.0084 | 0.46 | NO
101 | SLC16A3 | SLC16A3 | SLC16A3 | 7910 | -0.00084 | 0.44 | NO
102 | SUCLG2 | SUCLG2 | SUCLG2 | 8054 | -0.0034 | 0.43 | NO
103 | PDP2 | PDP2 | PDP2 | 8117 | -0.0046 | 0.42 | NO
104 | UQCRH | UQCRH | UQCRH | 8307 | -0.0079 | 0.42 | NO
105 | LDHB | LDHB | LDHB | 9208 | -0.026 | 0.37 | NO
106 | IDH1 | IDH1 | IDH1 | 11738 | -0.086 | 0.23 | NO
107 | ETFDH | ETFDH | ETFDH | 12287 | -0.1 | 0.21 | NO
108 | UCP2 | UCP2 | UCP2 | 12461 | -0.11 | 0.2 | NO
109 | SLC16A8 | SLC16A8 | SLC16A8 | 13050 | -0.13 | 0.18 | NO
110 | L2HGDH | L2HGDH | L2HGDH | 14268 | -0.19 | 0.12 | NO
111 | PDP1 | PDP1 | PDP1 | 15683 | -0.29 | 0.057 | NO
112 | SLC16A1 | SLC16A1 | SLC16A1 | 15872 | -0.31 | 0.064 | NO
113 | PDK4 | PDK4 | PDK4 | 16057 | -0.33 | 0.072 | NO
114 | UCP3 | UCP3 | UCP3 | 16269 | -0.35 | 0.08 | NO
115 | PDK3 | PDK3 | PDK3 | 16712 | -0.41 | 0.078 | NO

Figure S23. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG OXIDATIVE PHOSPHORYLATION.

Figure S24. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG OXIDATIVE PHOSPHORYLATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS

Table S13. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | MTFMT | MTFMT | MTFMT | 784 | 0.27 | 0.035 | YES
2 | TARSL2 | TARSL2 | TARSL2 | 1034 | 0.23 | 0.09 | YES
3 | IARS | IARS | IARS | 1345 | 0.2 | 0.13 | YES
4 | CARS2 | CARS2 | CARS2 | 1516 | 0.19 | 0.18 | YES
5 | WARS2 | WARS2 | WARS2 | 1641 | 0.18 | 0.22 | YES
6 | SARS2 | SARS2 | SARS2 | 2018 | 0.16 | 0.25 | YES
7 | AARS | AARS | AARS | 2524 | 0.13 | 0.26 | YES
8 | MARS2 | MARS2 | MARS2 | 2878 | 0.12 | 0.27 | YES
9 | LARS | LARS | LARS | 2902 | 0.12 | 0.31 | YES
10 | DARS2 | DARS2 | DARS2 | 2908 | 0.11 | 0.34 | YES
11 | KARS | KARS | KARS | 3196 | 0.1 | 0.36 | YES
12 | FARS2 | FARS2 | FARS2 | 3263 | 0.1 | 0.38 | YES
13 | EARS2 | EARS2 | EARS2 | 3503 | 0.095 | 0.4 | YES
14 | IARS2 | IARS2 | IARS2 | 4148 | 0.077 | 0.38 | YES
15 | GARS | GARS | GARS | 4460 | 0.069 | 0.39 | YES
16 | CARS | CARS | CARS | 4521 | 0.067 | 0.4 | YES
17 | EPRS | EPRS | EPRS | 4781 | 0.062 | 0.41 | YES
18 | NARS | NARS | NARS | 4961 | 0.058 | 0.41 | YES
19 | RARS | RARS | RARS | 5188 | 0.053 | 0.42 | YES
20 | QARS | QARS | QARS | 5300 | 0.05 | 0.43 | YES
21 | FARSA | FARSA | FARSA | 5327 | 0.05 | 0.44 | YES
22 | TARS | TARS | TARS | 5659 | 0.043 | 0.43 | NO
23 | DARS | DARS | DARS | 5901 | 0.038 | 0.43 | NO
24 | VARS2 | VARS2 | VARS2 | 6335 | 0.03 | 0.42 | NO
25 | AARS2 | AARS2 | AARS2 | 6344 | 0.03 | 0.42 | NO
26 | VARS | VARS | VARS | 7256 | 0.012 | 0.38 | NO
27 | HARS2 | HARS2 | HARS2 | 7301 | 0.011 | 0.38 | NO
28 | TARS2 | TARS2 | TARS2 | 7803 | 0.0011 | 0.35 | NO
29 | YARS2 | YARS2 | YARS2 | 7960 | -0.0017 | 0.34 | NO
30 | MARS | MARS | MARS | 8140 | -0.0051 | 0.33 | NO
31 | SARS | SARS | SARS | 8586 | -0.013 | 0.31 | NO
32 | YARS | YARS | YARS | 8623 | -0.014 | 0.32 | NO
33 | FARSB | FARSB | FARSB | 8683 | -0.015 | 0.32 | NO
34 | LARS2 | LARS2 | LARS2 | 8917 | -0.02 | 0.31 | NO
35 | SEPSECS | SEPSECS | SEPSECS | 9605 | -0.035 | 0.28 | NO
36 | PSTK | PSTK | PSTK | 9764 | -0.038 | 0.28 | NO
37 | RARS2 | RARS2 | RARS2 | 10182 | -0.048 | 0.28 | NO
38 | HARS | HARS | HARS | 10212 | -0.048 | 0.29 | NO
39 | WARS | WARS | WARS | 12356 | -0.11 | 0.2 | NO
40 | NARS2 | NARS2 | NARS2 | 13364 | -0.14 | 0.19 | NO
41 | PARS2 | PARS2 | PARS2 | 15242 | -0.26 | 0.16 | NO

Figure S25. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS.

Figure S26. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG ALZHEIMERS DISEASE

Table S14. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | ITPKA | ITPKA | ITPKA | 46 | 0.64 | 0.19 | YES
2 | VN1R1 | VN1R1 | VN1R1 | 398 | 0.35 | 0.28 | YES
3 | AKT3 | AKT3 | AKT3 | 579 | 0.31 | 0.36 | YES
4 | CFB | CFB | CFB | 1427 | 0.2 | 0.38 | YES
5 | PLD1 | PLD1 | PLD1 | 2339 | 0.14 | 0.37 | YES
6 | NFKBIL1 | NFKBIL1 | NFKBIL1 | 2485 | 0.13 | 0.4 | YES
7 | PITX2 | PITX2 | PITX2 | 2513 | 0.13 | 0.44 | YES
8 | NFKBIB | NFKBIB | NFKBIB | 2808 | 0.12 | 0.46 | YES
9 | AKT2 | AKT2 | AKT2 | 3542 | 0.094 | 0.44 | YES
10 | ITPKB | ITPKB | ITPKB | 3660 | 0.09 | 0.47 | YES
11 | NFKB1 | NFKB1 | NFKB1 | 3846 | 0.085 | 0.48 | YES
12 | NFKBIE | NFKBIE | NFKBIE | 4256 | 0.074 | 0.48 | NO
13 | GNAQ | GNAQ | GNAQ | 4779 | 0.062 | 0.47 | NO
14 | PIK3CB | PIK3CB | PIK3CB | 6304 | 0.03 | 0.4 | NO
15 | PHKA2 | PHKA2 | PHKA2 | 6555 | 0.026 | 0.39 | NO
16 | PDK1 | PDK1 | PDK1 | 6660 | 0.023 | 0.39 | NO
17 | ITPR2 | ITPR2 | ITPR2 | 6882 | 0.019 | 0.38 | NO
18 | PLD3 | PLD3 | PLD3 | 6941 | 0.018 | 0.39 | NO
19 | AKT1 | AKT1 | AKT1 | 8860 | -0.019 | 0.29 | NO
20 | ITPR3 | ITPR3 | ITPR3 | 9732 | -0.038 | 0.25 | NO
21 | PLD2 | PLD2 | PLD2 | 9926 | -0.042 | 0.25 | NO
22 | NFKB2 | NFKB2 | NFKB2 | 10580 | -0.057 | 0.23 | NO
23 | IKBKG | IKBKG | IKBKG | 10600 | -0.057 | 0.25 | NO
24 | DAG1 | DAG1 | DAG1 | 10945 | -0.065 | 0.25 | NO
25 | ADRBK1 | ADRBK1 | ADRBK1 | 11855 | -0.089 | 0.23 | NO
26 | NFKBIA | NFKBIA | NFKBIA | 13094 | -0.13 | 0.2 | NO
27 | ITPR1 | ITPR1 | ITPR1 | 15272 | -0.26 | 0.16 | NO

Figure S27. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ALZHEIMERS DISEASE.

Figure S28. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ALZHEIMERS DISEASE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PARKINSONS DISEASE

Table S15. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | IGFBP1 | IGFBP1 | IGFBP1 | 185 | 0.46 | 0.16 | YES
2 | EXOSC5 | EXOSC5 | EXOSC5 | 924 | 0.25 | 0.22 | YES
3 | DDIT3 | DDIT3 | DDIT3 | 1327 | 0.2 | 0.27 | YES
4 | ATF3 | ATF3 | ATF3 | 1500 | 0.19 | 0.33 | YES
5 | EXOSC8 | EXOSC8 | EXOSC8 | 1651 | 0.18 | 0.39 | YES
6 | CCL2 | CCL2 | CCL2 | 2600 | 0.13 | 0.39 | YES
7 | HSPA5 | HSPA5 | HSPA5 | 2844 | 0.12 | 0.42 | YES
8 | DIS3 | DIS3 | DIS3 | 3103 | 0.11 | 0.44 | YES
9 | HERPUD1 | HERPUD1 | HERPUD1 | 3710 | 0.088 | 0.44 | YES
10 | EXOSC2 | EXOSC2 | EXOSC2 | 3794 | 0.086 | 0.47 | YES
11 | EXOSC3 | EXOSC3 | EXOSC3 | 4579 | 0.066 | 0.45 | YES
12 | ASNS | ASNS | ASNS | 4647 | 0.064 | 0.47 | YES
13 | EXOSC6 | EXOSC6 | EXOSC6 | 4793 | 0.061 | 0.49 | YES
14 | PARN | PARN | PARN | 5607 | 0.044 | 0.46 | NO
15 | ATF6 | ATF6 | ATF6 | 6241 | 0.031 | 0.44 | NO
16 | EIF2S1 | EIF2S1 | EIF2S1 | 6604 | 0.024 | 0.43 | NO
17 | IL8 | IL8 | IL8 | 7769 | 0.0017 | 0.36 | NO
18 | NFYA | NFYA | NFYA | 7853 | 0.00012 | 0.36 | NO
19 | EXOSC9 | EXOSC9 | EXOSC9 | 8162 | -0.0054 | 0.34 | NO
20 | KHSRP | KHSRP | KHSRP | 8790 | -0.017 | 0.32 | NO
21 | NFYB | NFYB | NFYB | 8802 | -0.017 | 0.32 | NO
22 | ATF4 | ATF4 | ATF4 | 10617 | -0.058 | 0.24 | NO
23 | DCP2 | DCP2 | DCP2 | 11000 | -0.066 | 0.25 | NO
24 | EXOSC1 | EXOSC1 | EXOSC1 | 11255 | -0.072 | 0.26 | NO
25 | EIF2AK3 | EIF2AK3 | EIF2AK3 | 11525 | -0.08 | 0.28 | NO
26 | EXOSC7 | EXOSC7 | EXOSC7 | 11853 | -0.089 | 0.29 | NO
27 | EXOSC4 | EXOSC4 | EXOSC4 | 13294 | -0.14 | 0.27 | NO

Figure S29. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PARKINSONS DISEASE.

Figure S30. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PARKINSONS DISEASE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG HUNTINGTONS DISEASE

Table S16. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | NDUFA8 | NDUFA8 | NDUFA8 | 412 | 0.35 | 0.006 | YES
2 | UQCRFS1 | UQCRFS1 | UQCRFS1 | 504 | 0.32 | 0.028 | YES
3 | NDUFB5 | NDUFB5 | NDUFB5 | 634 | 0.29 | 0.045 | YES
4 | COX5A | COX5A | COX5A | 713 | 0.28 | 0.064 | YES
5 | COX7B | COX7B | COX7B | 746 | 0.27 | 0.084 | YES
6 | ATP5G1 | ATP5G1 | ATP5G1 | 752 | 0.27 | 0.11 | YES
7 | COX6B1 | COX6B1 | COX6B1 | 875 | 0.25 | 0.12 | YES
8 | CYCS | CYCS | CYCS | 879 | 0.25 | 0.14 | YES
9 | NDUFA12 | NDUFA12 | NDUFA12 | 926 | 0.25 | 0.16 | YES
10 | ATP5D | ATP5D | ATP5D | 972 | 0.24 | 0.18 | YES
11 | SDHA | SDHA | SDHA | 992 | 0.24 | 0.2 | YES
12 | NDUFS4 | NDUFS4 | NDUFS4 | 1091 | 0.23 | 0.21 | YES
13 | NDUFS3 | NDUFS3 | NDUFS3 | 1092 | 0.23 | 0.23 | YES
14 | ATP5B | ATP5B | ATP5B | 1122 | 0.22 | 0.24 | YES
15 | COX5B | COX5B | COX5B | 1157 | 0.22 | 0.26 | YES
16 | NDUFB6 | NDUFB6 | NDUFB6 | 1217 | 0.22 | 0.28 | YES
17 | ATP5O | ATP5O | ATP5O | 1233 | 0.21 | 0.29 | YES
18 | SDHD | SDHD | SDHD | 1319 | 0.2 | 0.3 | YES
19 | NDUFV3 | NDUFV3 | NDUFV3 | 1337 | 0.2 | 0.32 | YES
20 | ATP5J | ATP5J | ATP5J | 1393 | 0.2 | 0.33 | YES
21 | ATP5C1 | ATP5C1 | ATP5C1 | 1394 | 0.2 | 0.35 | YES
22 | UQCRB | UQCRB | UQCRB | 1438 | 0.19 | 0.36 | YES
23 | COX8A | COX8A | COX8A | 1447 | 0.19 | 0.38 | YES
24 | NDUFA6 | NDUFA6 | NDUFA6 | 1523 | 0.19 | 0.39 | YES
25 | ATP5A1 | ATP5A1 | ATP5A1 | 1551 | 0.18 | 0.4 | YES
26 | UQCR11 | UQCR11 | UQCR11 | 1570 | 0.18 | 0.42 | YES
27 | ATP5L | ATP5L | ATP5L | 1751 | 0.17 | 0.42 | YES
28 | COX7C | COX7C | COX7C | 1780 | 0.17 | 0.44 | YES
29 | UQCRC2 | UQCRC2 | UQCRC2 | 1798 | 0.17 | 0.45 | YES
30 | COX4I1 | COX4I1 | COX4I1 | 1865 | 0.16 | 0.46 | YES
31 | COX6A1 | COX6A1 | COX6A1 | 1921 | 0.16 | 0.47 | YES
32 | NDUFA1 | NDUFA1 | NDUFA1 | 1988 | 0.16 | 0.48 | YES
33 | NDUFA4 | NDUFA4 | NDUFA4 | 1991 | 0.16 | 0.49 | YES
34 | CYC1 | CYC1 | CYC1 | 2004 | 0.16 | 0.5 | YES
35 | NDUFA3 | NDUFA3 | NDUFA3 | 2052 | 0.15 | 0.51 | YES
36 | ATP5J2 | ATP5J2 | ATP5J2 | 2083 | 0.15 | 0.52 | YES
37 | NDUFS7 | NDUFS7 | NDUFS7 | 2100 | 0.15 | 0.54 | YES
38 | NDUFB2 | NDUFB2 | NDUFB2 | 2130 | 0.15 | 0.55 | YES
39 | UQCRC1 | UQCRC1 | UQCRC1 | 2162 | 0.15 | 0.56 | YES
40 | ATP5H | ATP5H | ATP5H | 2171 | 0.15 | 0.57 | YES
41 | NDUFA10 | NDUFA10 | NDUFA10 | 2182 | 0.15 | 0.58 | YES
42 | NDUFB3 | NDUFB3 | NDUFB3 | 2202 | 0.15 | 0.59 | YES
43 | ATP5I | ATP5I | ATP5I | 2217 | 0.14 | 0.6 | YES
44 | NDUFB9 | NDUFB9 | NDUFB9 | 2222 | 0.14 | 0.61 | YES
45 | NDUFA13 | NDUFA13 | NDUFA13 | 2362 | 0.14 | 0.62 | YES
46 | UQCRQ | UQCRQ | UQCRQ | 2398 | 0.14 | 0.63 | YES
47 | NDUFB7 | NDUFB7 | NDUFB7 | 2479 | 0.13 | 0.63 | YES
48 | SDHC | SDHC | SDHC | 2757 | 0.12 | 0.63 | YES
49 | NDUFB10 | NDUFB10 | NDUFB10 | 2825 | 0.12 | 0.63 | YES
50 | NDUFS8 | NDUFS8 | NDUFS8 | 2826 | 0.12 | 0.64 | YES
51 | NDUFS2 | NDUFS2 | NDUFS2 | 2829 | 0.12 | 0.65 | YES
52 | NDUFS1 | NDUFS1 | NDUFS1 | 2863 | 0.12 | 0.66 | YES
53 | NDUFV2 | NDUFV2 | NDUFV2 | 2974 | 0.11 | 0.66 | YES
54 | COX6C | COX6C | COX6C | 3073 | 0.11 | 0.67 | YES
55 | NDUFAB1 | NDUFAB1 | NDUFAB1 | 3132 | 0.11 | 0.67 | YES
56 | SDHB | SDHB | SDHB | 3291 | 0.1 | 0.67 | YES
57 | NDUFA7 | NDUFA7 | NDUFA7 | 3304 | 0.1 | 0.68 | YES
58 | NDUFA9 | NDUFA9 | NDUFA9 | 3360 | 0.1 | 0.68 | YES
59 | NDUFV1 | NDUFV1 | NDUFV1 | 3632 | 0.091 | 0.68 | YES
60 | ATP5E | ATP5E | ATP5E | 3790 | 0.086 | 0.68 | YES
61 | NDUFC1 | NDUFC1 | NDUFC1 | 3839 | 0.085 | 0.68 | YES
62 | NDUFS6 | NDUFS6 | NDUFS6 | 4088 | 0.078 | 0.67 | YES
63 | ATP5F1 | ATP5F1 | ATP5F1 | 4255 | 0.074 | 0.67 | YES
64 | NDUFA2 | NDUFA2 | NDUFA2 | 4258 | 0.074 | 0.68 | YES
65 | NDUFA11 | NDUFA11 | NDUFA11 | 4271 | 0.074 | 0.68 | YES
66 | NDUFB4 | NDUFB4 | NDUFB4 | 4371 | 0.071 | 0.68 | YES
67 | ETFA | ETFA | ETFA | 4372 | 0.071 | 0.69 | YES
68 | NDUFB1 | NDUFB1 | NDUFB1 | 4788 | 0.061 | 0.67 | NO
69 | ETFB | ETFB | ETFB | 5219 | 0.052 | 0.65 | NO
70 | NDUFB8 | NDUFB8 | NDUFB8 | 5220 | 0.052 | 0.65 | NO
71 | NDUFA5 | NDUFA5 | NDUFA5 | 5714 | 0.042 | 0.63 | NO
72 | COX7A2L | COX7A2L | COX7A2L | 5827 | 0.04 | 0.63 | NO
73 | NDUFS5 | NDUFS5 | NDUFS5 | 6167 | 0.033 | 0.61 | NO
74 | NDUFC2 | NDUFC2 | NDUFC2 | 6181 | 0.033 | 0.61 | NO
75 | UQCRHL | UQCRHL | UQCRHL | 7431 | 0.0084 | 0.55 | NO
76 | UQCRH | UQCRH | UQCRH | 8307 | -0.0079 | 0.5 | NO
77 | ETFDH | ETFDH | ETFDH | 12287 | -0.1 | 0.28 | NO
78 | UCP2 | UCP2 | UCP2 | 12461 | -0.11 | 0.28 | NO
79 | UCP3 | UCP3 | UCP3 | 16269 | -0.35 | 0.1 | NO

Figure S31. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG HUNTINGTONS DISEASE.

Figure S32. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG HUNTINGTONS DISEASE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: ST GAQ PATHWAY

Table S17. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | IARS | IARS | IARS | 1345 | 0.2 | -0.012 | YES
2 | CARS2 | CARS2 | CARS2 | 1516 | 0.19 | 0.037 | YES
3 | WARS2 | WARS2 | WARS2 | 1641 | 0.18 | 0.085 | YES
4 | PPA2 | PPA2 | PPA2 | 1747 | 0.17 | 0.13 | YES
5 | AIMP2 | AIMP2 | AIMP2 | 1857 | 0.16 | 0.18 | YES
6 | SARS2 | SARS2 | SARS2 | 2018 | 0.16 | 0.22 | YES
7 | AARS | AARS | AARS | 2524 | 0.13 | 0.23 | YES
8 | MARS2 | MARS2 | MARS2 | 2878 | 0.12 | 0.25 | YES
9 | LARS | LARS | LARS | 2902 | 0.12 | 0.28 | YES
10 | DARS2 | DARS2 | DARS2 | 2908 | 0.11 | 0.32 | YES
11 | KARS | KARS | KARS | 3196 | 0.1 | 0.33 | YES
12 | FARS2 | FARS2 | FARS2 | 3263 | 0.1 | 0.36 | YES
13 | EARS2 | EARS2 | EARS2 | 3503 | 0.095 | 0.38 | YES
14 | IARS2 | IARS2 | IARS2 | 4148 | 0.077 | 0.36 | YES
15 | GARS | GARS | GARS | 4460 | 0.069 | 0.37 | YES
16 | CARS | CARS | CARS | 4521 | 0.067 | 0.39 | YES
17 | EPRS | EPRS | EPRS | 4781 | 0.062 | 0.39 | YES
18 | NARS | NARS | NARS | 4961 | 0.058 | 0.4 | YES
19 | RARS | RARS | RARS | 5188 | 0.053 | 0.4 | YES
20 | QARS | QARS | QARS | 5300 | 0.05 | 0.41 | YES
21 | FARSA | FARSA | FARSA | 5327 | 0.05 | 0.43 | YES
22 | TARS | TARS | TARS | 5659 | 0.043 | 0.42 | NO
23 | DARS | DARS | DARS | 5901 | 0.038 | 0.42 | NO
24 | VARS2 | VARS2 | VARS2 | 6335 | 0.03 | 0.4 | NO
25 | AARS2 | AARS2 | AARS2 | 6344 | 0.03 | 0.41 | NO
26 | AIMP1 | AIMP1 | AIMP1 | 6955 | 0.018 | 0.39 | NO
27 | VARS | VARS | VARS | 7256 | 0.012 | 0.37 | NO
28 | HARS2 | HARS2 | HARS2 | 7301 | 0.011 | 0.37 | NO
29 | TARS2 | TARS2 | TARS2 | 7803 | 0.0011 | 0.35 | NO
30 | EEF1E1 | EEF1E1 | EEF1E1 | 7877 | -0.00032 | 0.34 | NO
31 | YARS2 | YARS2 | YARS2 | 7960 | -0.0017 | 0.34 | NO
32 | MARS | MARS | MARS | 8140 | -0.0051 | 0.33 | NO
33 | SARS | SARS | SARS | 8586 | -0.013 | 0.31 | NO
34 | YARS | YARS | YARS | 8623 | -0.014 | 0.31 | NO
35 | FARSB | FARSB | FARSB | 8683 | -0.015 | 0.31 | NO
36 | LARS2 | LARS2 | LARS2 | 8917 | -0.02 | 0.31 | NO
37 | RARS2 | RARS2 | RARS2 | 10182 | -0.048 | 0.25 | NO
38 | HARS | HARS | HARS | 10212 | -0.048 | 0.26 | NO
39 | PPA1 | PPA1 | PPA1 | 10307 | -0.05 | 0.28 | NO
40 | WARS | WARS | WARS | 12356 | -0.11 | 0.19 | NO
41 | NARS2 | NARS2 | NARS2 | 13364 | -0.14 | 0.18 | NO
42 | PARS2 | PARS2 | PARS2 | 15242 | -0.26 | 0.16 | NO

Figure S33. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: ST GAQ PATHWAY.

Figure S34. Get High-res Image For the top 5 core enriched genes in the pathway: ST GAQ PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID MTOR 4PATHWAY

Table S18. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | ADHFE1 | ADHFE1 | ADHFE1 | 176 | 0.46 | 0.06 | YES
2 | IDH3A | IDH3A | IDH3A | 415 | 0.35 | 0.1 | YES
3 | NNT | NNT | NNT | 482 | 0.33 | 0.15 | YES
4 | SDHA | SDHA | SDHA | 992 | 0.24 | 0.16 | YES
5 | CS | CS | CS | 996 | 0.24 | 0.19 | YES
6 | PDHA1 | PDHA1 | PDHA1 | 1024 | 0.24 | 0.22 | YES
7 | SUCLG1 | SUCLG1 | SUCLG1 | 1033 | 0.23 | 0.26 | YES
8 | ACO2 | ACO2 | ACO2 | 1149 | 0.22 | 0.29 | YES
9 | SUCLA2 | SUCLA2 | SUCLA2 | 1183 | 0.22 | 0.32 | YES
10 | SDHD | SDHD | SDHD | 1319 | 0.2 | 0.34 | YES
11 | OGDH | OGDH | OGDH | 1359 | 0.2 | 0.37 | YES
12 | DLAT | DLAT | DLAT | 1579 | 0.18 | 0.39 | YES
13 | IDH2 | IDH2 | IDH2 | 1631 | 0.18 | 0.41 | YES
14 | FH | FH | FH | 1795 | 0.17 | 0.43 | YES
15 | LDHA | LDHA | LDHA | 1839 | 0.17 | 0.45 | YES
16 | DLD | DLD | DLD | 1922 | 0.16 | 0.47 | YES
17 | MDH2 | MDH2 | MDH2 | 2178 | 0.15 | 0.48 | YES
18 | PDHX | PDHX | PDHX | 2247 | 0.14 | 0.5 | YES
19 | SDHC | SDHC | SDHC | 2757 | 0.12 | 0.49 | NO
20 | PDPR | PDPR | PDPR | 3273 | 0.1 | 0.47 | NO
21 | SDHB | SDHB | SDHB | 3291 | 0.1 | 0.49 | NO
22 | DLST | DLST | DLST | 3612 | 0.092 | 0.48 | NO
23 | D2HGDH | D2HGDH | D2HGDH | 3688 | 0.089 | 0.49 | NO
24 | IDH3G | IDH3G | IDH3G | 5192 | 0.053 | 0.42 | NO
25 | BSG | BSG | BSG | 5277 | 0.051 | 0.42 | NO
26 | IDH3B | IDH3B | IDH3B | 5416 | 0.048 | 0.42 | NO
27 | PDK2 | PDK2 | PDK2 | 6286 | 0.03 | 0.38 | NO
28 | PDK1 | PDK1 | PDK1 | 6660 | 0.023 | 0.36 | NO
29 | PDHB | PDHB | PDHB | 6768 | 0.021 | 0.36 | NO
30 | SLC16A3 | SLC16A3 | SLC16A3 | 7910 | -0.00084 | 0.29 | NO
31 | SUCLG2 | SUCLG2 | SUCLG2 | 8054 | -0.0034 | 0.29 | NO
32 | PDP2 | PDP2 | PDP2 | 8117 | -0.0046 | 0.28 | NO
33 | LDHB | LDHB | LDHB | 9208 | -0.026 | 0.23 | NO
34 | IDH1 | IDH1 | IDH1 | 11738 | -0.086 | 0.1 | NO
35 | SLC16A8 | SLC16A8 | SLC16A8 | 13050 | -0.13 | 0.048 | NO
36 | L2HGDH | L2HGDH | L2HGDH | 14268 | -0.19 | 0.0094 | NO
37 | PDP1 | PDP1 | PDP1 | 15683 | -0.29 | -0.025 | NO
38 | SLC16A1 | SLC16A1 | SLC16A1 | 15872 | -0.31 | 0.012 | NO
39 | PDK4 | PDK4 | PDK4 | 16057 | -0.33 | 0.051 | NO
40 | PDK3 | PDK3 | PDK3 | 16712 | -0.41 | 0.078 | NO

Figure S35. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID MTOR 4PATHWAY.

Figure S36. Get High-res Image For the top 5 core enriched genes in the pathway: PID MTOR 4PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME TRANSLATION

Table S19. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | OGDHL | OGDHL | OGDHL | 110 | 0.53 | 0.094 | YES
2 | IDH3A | IDH3A | IDH3A | 415 | 0.35 | 0.14 | YES
3 | ACO1 | ACO1 | ACO1 | 418 | 0.35 | 0.21 | YES
4 | SDHA | SDHA | SDHA | 992 | 0.24 | 0.22 | YES
5 | CS | CS | CS | 996 | 0.24 | 0.27 | YES
6 | PDHA1 | PDHA1 | PDHA1 | 1024 | 0.24 | 0.31 | YES
7 | SUCLG1 | SUCLG1 | SUCLG1 | 1033 | 0.23 | 0.35 | YES
8 | ACO2 | ACO2 | ACO2 | 1149 | 0.22 | 0.39 | YES
9 | SUCLA2 | SUCLA2 | SUCLA2 | 1183 | 0.22 | 0.43 | YES
10 | SDHD | SDHD | SDHD | 1319 | 0.2 | 0.46 | YES
11 | OGDH | OGDH | OGDH | 1359 | 0.2 | 0.5 | YES
12 | DLAT | DLAT | DLAT | 1579 | 0.18 | 0.52 | YES
13 | IDH2 | IDH2 | IDH2 | 1631 | 0.18 | 0.55 | YES
14 | FH | FH | FH | 1795 | 0.17 | 0.57 | YES
15 | DLD | DLD | DLD | 1922 | 0.16 | 0.6 | YES
16 | MDH1 | MDH1 | MDH1 | 2176 | 0.15 | 0.61 | YES
17 | MDH2 | MDH2 | MDH2 | 2178 | 0.15 | 0.64 | YES
18 | SDHC | SDHC | SDHC | 2757 | 0.12 | 0.63 | NO
19 | SDHB | SDHB | SDHB | 3291 | 0.1 | 0.62 | NO
20 | DLST | DLST | DLST | 3612 | 0.092 | 0.62 | NO
21 | ACLY | ACLY | ACLY | 4527 | 0.067 | 0.58 | NO
22 | IDH3G | IDH3G | IDH3G | 5192 | 0.053 | 0.55 | NO
23 | IDH3B | IDH3B | IDH3B | 5416 | 0.048 | 0.55 | NO
24 | PDHB | PDHB | PDHB | 6768 | 0.021 | 0.48 | NO
25 | SUCLG2 | SUCLG2 | SUCLG2 | 8054 | -0.0034 | 0.41 | NO
26 | IDH1 | IDH1 | IDH1 | 11738 | -0.086 | 0.22 | NO
27 | PCK2 | PCK2 | PCK2 | 13641 | -0.16 | 0.15 | NO
28 | PCK1 | PCK1 | PCK1 | 15217 | -0.25 | 0.11 | NO
29 | PC | PC | PC | 15610 | -0.28 | 0.14 | NO

Figure S37. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME TRANSLATION.

Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TRANSLATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE

Table S20. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | NDUFA8 | NDUFA8 | NDUFA8 | 412 | 0.35 | 0.014 | YES
2 | UQCRFS1 | UQCRFS1 | UQCRFS1 | 504 | 0.32 | 0.044 | YES
3 | NDUFB5 | NDUFB5 | NDUFB5 | 634 | 0.29 | 0.069 | YES
4 | COX5A | COX5A | COX5A | 713 | 0.28 | 0.094 | YES
5 | COX7B | COX7B | COX7B | 746 | 0.27 | 0.12 | YES
6 | COX6B1 | COX6B1 | COX6B1 | 875 | 0.25 | 0.14 | YES
7 | CYCS | CYCS | CYCS | 879 | 0.25 | 0.17 | YES
8 | NDUFA12 | NDUFA12 | NDUFA12 | 926 | 0.25 | 0.19 | YES
9 | SDHA | SDHA | SDHA | 992 | 0.24 | 0.21 | YES
10 | NDUFS4 | NDUFS4 | NDUFS4 | 1091 | 0.23 | 0.23 | YES
11 | NDUFS3 | NDUFS3 | NDUFS3 | 1092 | 0.23 | 0.26 | YES
12 | COX5B | COX5B | COX5B | 1157 | 0.22 | 0.28 | YES
13 | NDUFB6 | NDUFB6 | NDUFB6 | 1217 | 0.22 | 0.3 | YES
14 | SDHD | SDHD | SDHD | 1319 | 0.2 | 0.31 | YES
15 | NDUFV3 | NDUFV3 | NDUFV3 | 1337 | 0.2 | 0.33 | YES
16 | UQCRB | UQCRB | UQCRB | 1438 | 0.19 | 0.35 | YES
17 | COX8A | COX8A | COX8A | 1447 | 0.19 | 0.37 | YES
18 | NDUFA6 | NDUFA6 | NDUFA6 | 1523 | 0.19 | 0.39 | YES
19 | UQCR11 | UQCR11 | UQCR11 | 1570 | 0.18 | 0.4 | YES
20 | COX7C | COX7C | COX7C | 1780 | 0.17 | 0.41 | YES
21 | UQCRC2 | UQCRC2 | UQCRC2 | 1798 | 0.17 | 0.43 | YES
22 | COX4I1 | COX4I1 | COX4I1 | 1865 | 0.16 | 0.44 | YES
23 | COX6A1 | COX6A1 | COX6A1 | 1921 | 0.16 | 0.46 | YES
24 | NDUFA1 | NDUFA1 | NDUFA1 | 1988 | 0.16 | 0.47 | YES
25 | NDUFA4 | NDUFA4 | NDUFA4 | 1991 | 0.16 | 0.48 | YES
26 | CYC1 | CYC1 | CYC1 | 2004 | 0.16 | 0.5 | YES
27 | NDUFA3 | NDUFA3 | NDUFA3 | 2052 | 0.15 | 0.51 | YES
28 | NDUFS7 | NDUFS7 | NDUFS7 | 2100 | 0.15 | 0.53 | YES
29 | NDUFB2 | NDUFB2 | NDUFB2 | 2130 | 0.15 | 0.54 | YES
30 | UQCRC1 | UQCRC1 | UQCRC1 | 2162 | 0.15 | 0.56 | YES
31 | NDUFA10 | NDUFA10 | NDUFA10 | 2182 | 0.15 | 0.57 | YES
32 | NDUFB3 | NDUFB3 | NDUFB3 | 2202 | 0.15 | 0.59 | YES
33 | NDUFB9 | NDUFB9 | NDUFB9 | 2222 | 0.14 | 0.6 | YES
34 | NDUFA13 | NDUFA13 | NDUFA13 | 2362 | 0.14 | 0.61 | YES
35 | UQCRQ | UQCRQ | UQCRQ | 2398 | 0.14 | 0.62 | YES
36 | NDUFB7 | NDUFB7 | NDUFB7 | 2479 | 0.13 | 0.63 | YES
37 | SDHC | SDHC | SDHC | 2757 | 0.12 | 0.63 | YES
38 | NDUFB10 | NDUFB10 | NDUFB10 | 2825 | 0.12 | 0.64 | YES
39 | NDUFS8 | NDUFS8 | NDUFS8 | 2826 | 0.12 | 0.65 | YES
40 | NDUFS2 | NDUFS2 | NDUFS2 | 2829 | 0.12 | 0.66 | YES
41 | NDUFS1 | NDUFS1 | NDUFS1 | 2863 | 0.12 | 0.67 | YES
42 | NDUFV2 | NDUFV2 | NDUFV2 | 2974 | 0.11 | 0.68 | YES
43 | COX6C | COX6C | COX6C | 3073 | 0.11 | 0.68 | YES
44 | NDUFAB1 | NDUFAB1 | NDUFAB1 | 3132 | 0.11 | 0.69 | YES
45 | SDHB | SDHB | SDHB | 3291 | 0.1 | 0.69 | YES
46 | NDUFA7 | NDUFA7 | NDUFA7 | 3304 | 0.1 | 0.7 | YES
47 | NDUFA9 | NDUFA9 | NDUFA9 | 3360 | 0.1 | 0.71 | YES
48 | NDUFV1 | NDUFV1 | NDUFV1 | 3632 | 0.091 | 0.71 | YES
49 | NDUFC1 | NDUFC1 | NDUFC1 | 3839 | 0.085 | 0.7 | YES
50 | NDUFS6 | NDUFS6 | NDUFS6 | 4088 | 0.078 | 0.7 | YES
51 | NDUFA2 | NDUFA2 | NDUFA2 | 4258 | 0.074 | 0.7 | YES
52 | NDUFA11 | NDUFA11 | NDUFA11 | 4271 | 0.074 | 0.7 | YES
53 | NDUFB4 | NDUFB4 | NDUFB4 | 4371 | 0.071 | 0.71 | YES
54 | ETFA | ETFA | ETFA | 4372 | 0.071 | 0.71 | YES
55 | NDUFB1 | NDUFB1 | NDUFB1 | 4788 | 0.061 | 0.7 | NO
56 | ETFB | ETFB | ETFB | 5219 | 0.052 | 0.68 | NO
57 | NDUFB8 | NDUFB8 | NDUFB8 | 5220 | 0.052 | 0.68 | NO
58 | NDUFA5 | NDUFA5 | NDUFA5 | 5714 | 0.042 | 0.66 | NO
59 | COX7A2L | COX7A2L | COX7A2L | 5827 | 0.04 | 0.66 | NO
60 | NDUFS5 | NDUFS5 | NDUFS5 | 6167 | 0.033 | 0.64 | NO
61 | NDUFC2 | NDUFC2 | NDUFC2 | 6181 | 0.033 | 0.65 | NO
62 | UQCRHL | UQCRHL | UQCRHL | 7431 | 0.0084 | 0.58 | NO
63 | UQCRH | UQCRH | UQCRH | 8307 | -0.0079 | 0.53 | NO
64 | ETFDH | ETFDH | ETFDH | 12287 | -0.1 | 0.32 | NO

Figure S39. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE.

Figure S40. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

For the top enriched genes, if you want to check whether they are

- up-regulated, please check the list of up-regulated genes

- down-regulated, please check the list of down-regulated genes

Expression level

For the top enriched genes, if you want to check whether they are

- highly expressed genes, please check the list of high (top 30%) expressed genes

- low expressed genes, please check the list of low (bottom 30%) expressed genes

An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap

Significant gene list

For the top enriched genes, if you want to check whether they are

- significantly differently expressed genes by eBayes lm fit, please check the list of significant genes

Subtype clus3 enriched pathways

Table 5. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus3. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION | 234 | genes.ES.table | 0.64 | 1.6 | 0.011 | 0.2 | 0.92 | 0.48 | 0.16 | 0.41 | 0.12 | 0.022
KEGG CHEMOKINE SIGNALING PATHWAY | 183 | genes.ES.table | 0.66 | 1.8 | 0.002 | 0.21 | 0.56 | 0.42 | 0.16 | 0.35 | 0.059 | 0.06
KEGG ENDOCYTOSIS | 179 | genes.ES.table | 0.36 | 1.6 | 0.036 | 0.21 | 0.95 | 0.27 | 0.26 | 0.2 | 0.14 | 0.016
KEGG MTOR SIGNALING PATHWAY | 51 | genes.ES.table | 0.39 | 1.5 | 0.043 | 0.24 | 0.97 | 0.14 | 0.13 | 0.12 | 0.17 | 0.013
KEGG APOPTOSIS | 84 | genes.ES.table | 0.48 | 1.7 | 0.022 | 0.18 | 0.83 | 0.31 | 0.21 | 0.24 | 0.087 | 0.021
KEGG CELL ADHESION MOLECULES CAMS | 129 | genes.ES.table | 0.6 | 1.6 | 0.024 | 0.22 | 0.96 | 0.5 | 0.17 | 0.42 | 0.15 | 0.015
KEGG ANTIGEN PROCESSING AND PRESENTATION | 67 | genes.ES.table | 0.66 | 1.6 | 0.03 | 0.18 | 0.88 | 0.46 | 0.15 | 0.39 | 0.1 | 0.021
KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY | 89 | genes.ES.table | 0.67 | 1.8 | 0 | 0.24 | 0.45 | 0.34 | 0.13 | 0.29 | 0 | 0.065
KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY | 61 | genes.ES.table | 0.57 | 1.5 | 0.065 | 0.23 | 0.96 | 0.46 | 0.27 | 0.34 | 0.16 | 0.015
KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY | 56 | genes.ES.table | 0.56 | 2 | 0 | 0.33 | 0.16 | 0.38 | 0.25 | 0.28 | 0 | 0.081

genes ES table in pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION

Table S21. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | CD79A | CD79A | CD79A | 30 | 0.95 | 0.06 | YES
2 | CD79B | CD79B | CD79B | 51 | 0.89 | 0.12 | YES
3 | CD19 | CD19 | CD19 | 93 | 0.82 | 0.17 | YES
4 | PRKCB | PRKCB | PRKCB | 140 | 0.77 | 0.22 | YES
5 | RASGRP1 | RASGRP1 | RASGRP1 | 366 | 0.63 | 0.24 | YES
6 | BLK | BLK | BLK | 387 | 0.62 | 0.28 | YES
7 | BTK | BTK | BTK | 405 | 0.62 | 0.32 | YES
8 | PIK3CD | PIK3CD | PIK3CD | 604 | 0.54 | 0.35 | YES
9 | VAV1 | VAV1 | VAV1 | 622 | 0.54 | 0.38 | YES
10 | REL | REL | REL | 802 | 0.49 | 0.4 | YES
11 | CARD11 | CARD11 | CARD11 | 991 | 0.44 | 0.42 | YES
12 | RASGRP3 | RASGRP3 | RASGRP3 | 1147 | 0.42 | 0.44 | YES
13 | BLNK | BLNK | BLNK | 1587 | 0.35 | 0.44 | YES
14 | PSMB9 | PSMB9 | PSMB9 | 1841 | 0.32 | 0.45 | YES
15 | SYK | SYK | SYK | 2066 | 0.29 | 0.45 | YES
16 | FYN | FYN | FYN | 2329 | 0.26 | 0.46 | YES
17 | THEM4 | THEM4 | THEM4 | 2699 | 0.23 | 0.45 | YES
18 | PLCG2 | PLCG2 | PLCG2 | 2854 | 0.22 | 0.46 | YES
19 | PSMB10 | PSMB10 | PSMB10 | 2983 | 0.21 | 0.46 | YES
20 | LYN | LYN | LYN | 3058 | 0.2 | 0.47 | YES
21 | ITPR2 | ITPR2 | ITPR2 | 3079 | 0.2 | 0.48 | YES
22 | PSMB8 | PSMB8 | PSMB8 | 4018 | 0.15 | 0.44 | NO
23 | IKBKB | IKBKB | IKBKB | 4144 | 0.14 | 0.44 | NO
24 | SH3KBP1 | SH3KBP1 | SH3KBP1 | 4527 | 0.13 | 0.43 | NO
25 | AKT3 | AKT3 | AKT3 | 4602 | 0.13 | 0.44 | NO
26 | SOS1 | SOS1 | SOS1 | 4921 | 0.12 | 0.43 | NO
27 | PLCG1 | PLCG1 | PLCG1 | 5006 | 0.11 | 0.43 | NO
28 | NCK1 | NCK1 | NCK1 | 5080 | 0.11 | 0.43 | NO
29 | BCL10 | BCL10 | BCL10 | 5448 | 0.097 | 0.42 | NO
30 | MAP3K7 | MAP3K7 | MAP3K7 | 5552 | 0.094 | 0.42 | NO
31 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 5699 | 0.09 | 0.42 | NO
32 | ITPR3 | ITPR3 | ITPR3 | 5724 | 0.09 | 0.42 | NO
33 | CDKN1B | CDKN1B | CDKN1B | 5730 | 0.09 | 0.43 | NO
34 | CBLB | CBLB | CBLB | 5911 | 0.085 | 0.42 | NO
35 | NFKBIA | NFKBIA | NFKBIA | 6092 | 0.081 | 0.42 | NO
36 | CBL | CBL | CBL | 6102 | 0.081 | 0.42 | NO
37 | PSME4 | PSME4 | PSME4 | 6211 | 0.078 | 0.42 | NO
38 | MALT1 | MALT1 | MALT1 | 6423 | 0.073 | 0.41 | NO
39 | RICTOR | RICTOR | RICTOR | 6462 | 0.072 | 0.42 | NO
40 | PSMB2 | PSMB2 | PSMB2 | 6564 | 0.07 | 0.42 | NO
41 | NFKBIE | NFKBIE | NFKBIE | 6622 | 0.068 | 0.42 | NO
42 | RPS27A | RPS27A | RPS27A | 6857 | 0.063 | 0.41 | NO
43 | PDPK1 | PDPK1 | PDPK1 | 7024 | 0.06 | 0.4 | NO
44 | PSME2 | PSME2 | PSME2 | 7053 | 0.06 | 0.4 | NO
45 | AKT2 | AKT2 | AKT2 | 7055 | 0.06 | 0.41 | NO
46 | FOXO4 | FOXO4 | FOXO4 | 7208 | 0.056 | 0.4 | NO
47 | IKBKG | IKBKG | IKBKG | 7261 | 0.055 | 0.4 | NO
48 | FBXW11 | FBXW11 | FBXW11 | 7384 | 0.052 | 0.4 | NO
49 | STIM1 | STIM1 | STIM1 | 7413 | 0.052 | 0.4 | NO
50 | PSME1 | PSME1 | PSME1 | 7515 | 0.05 | 0.4 | NO
51 | UBA52 | UBA52 | UBA52 | 7532 | 0.05 | 0.4 | NO
52 | MTOR | MTOR | MTOR | 7612 | 0.048 | 0.4 | NO
53 | FOXO1 | FOXO1 | FOXO1 | 7694 | 0.047 | 0.4 | NO
54 | GRB2 | GRB2 | GRB2 | 7701 | 0.046 | 0.4 | NO
55 | ORAI1 | ORAI1 | ORAI1 | 7802 | 0.044 | 0.4 | NO
56 | TSC2 | TSC2 | TSC2 | 7902 | 0.042 | 0.4 | NO
57 | CUL1 | CUL1 | CUL1 | 7996 | 0.04 | 0.4 | NO
58 | PSMA4 | PSMA4 | PSMA4 | 8048 | 0.04 | 0.4 | NO
59 | FOXO3 | FOXO3 | FOXO3 | 8232 | 0.037 | 0.39 | NO
60 | PTEN | PTEN | PTEN | 8353 | 0.034 | 0.38 | NO
61 | CHUK | CHUK | CHUK | 8406 | 0.033 | 0.38 | NO
62 | CREB1 | CREB1 | CREB1 | 8753 | 0.028 | 0.36 | NO
63 | PSMD13 | PSMD13 | PSMD13 | 8761 | 0.028 | 0.37 | NO
64 | PSMD5 | PSMD5 | PSMD5 | 9301 | 0.019 | 0.34 | NO
65 | NFKBIB | NFKBIB | NFKBIB | 9396 | 0.017 | 0.33 | NO
66 | PSMA5 | PSMA5 | PSMA5 | 9401 | 0.017 | 0.33 | NO
67 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 9409 | 0.017 | 0.34 | NO
68 | PSMD10 | PSMD10 | PSMD10 | 9739 | 0.011 | 0.32 | NO
69 | PSMB1 | PSMB1 | PSMB1 | 9886 | 0.0087 | 0.31 | NO
70 | MDM2 | MDM2 | MDM2 | 9954 | 0.0077 | 0.31 | NO
71 | PSMC2 | PSMC2 | PSMC2 | 10114 | 0.0049 | 0.3 | NO
72 | RELA | RELA | RELA | 10186 | 0.0039 | 0.29 | NO
73 | NR4A1 | NR4A1 | NR4A1 | 10197 | 0.0036 | 0.29 | NO
74 | PSMD11 | PSMD11 | PSMD11 | 10232 | 0.003 | 0.29 | NO
75 | PSMB3 | PSMB3 | PSMB3 | 10329 | 0.0011 | 0.29 | NO
76 | PSMA2 | PSMA2 | PSMA2 | 10460 | -0.0012 | 0.28 | NO
77 | PSMA7 | PSMA7 | PSMA7 | 10541 | -0.0025 | 0.28 | NO
78 | PSMD12 | PSMD12 | PSMD12 | 10663 | -0.0049 | 0.27 | NO
79 | PSMD3 | PSMD3 | PSMD3 | 10703 | -0.0055 | 0.27 | NO
80 | PSMA1 | PSMA1 | PSMA1 | 10839 | -0.0078 | 0.26 | NO
81 | PSMD4 | PSMD4 | PSMD4 | 10862 | -0.0082 | 0.26 | NO
82 | SKP1 | SKP1 | SKP1 | 11050 | -0.011 | 0.25 | NO
83 | PSMF1 | PSMF1 | PSMF1 | 11208 | -0.014 | 0.24 | NO
84 | BTRC | BTRC | BTRC | 11320 | -0.016 | 0.24 | NO
85 | PSMC5 | PSMC5 | PSMC5 | 11348 | -0.017 | 0.24 | NO
86 | MLST8 | MLST8 | MLST8 | 11392 | -0.018 | 0.24 | NO
87 | PSMD1 | PSMD1 | PSMD1 | 11449 | -0.019 | 0.23 | NO
88 | GSK3A | GSK3A | GSK3A | 11493 | -0.02 | 0.23 | NO
89 | PSMC4 | PSMC4 | PSMC4 | 11567 | -0.021 | 0.23 | NO
90 | KRAS | KRAS | KRAS | 11599 | -0.021 | 0.23 | NO
91 | CASP9 | CASP9 | CASP9 | 11704 | -0.023 | 0.22 | NO
92 | PSMD6 | PSMD6 | PSMD6 | 11710 | -0.023 | 0.23 | NO
93 | PSMB4 | PSMB4 | PSMB4 | 11839 | -0.026 | 0.22 | NO
94 | HRAS | HRAS | HRAS | 11910 | -0.028 | 0.22 | NO
95 | PSMD7 | PSMD7 | PSMD7 | 12043 | -0.03 | 0.21 | NO
96 | PSMD2 | PSMD2 | PSMD2 | 12188 | -0.033 | 0.21 | NO
97 | CALM3 | CALM3 | CALM3 | 12242 | -0.035 | 0.21 | NO
98 | NRAS | NRAS | NRAS | 12308 | -0.036 | 0.21 | NO
99 | PSMC3 | PSMC3 | PSMC3 | 12313 | -0.036 | 0.21 | NO
100 | CALM1 | CALM1 | CALM1 | 12485 | -0.039 | 0.2 | NO
101 | CALM2 | CALM2 | CALM2 | 12515 | -0.04 | 0.2 | NO
102 | PSMA6 | PSMA6 | PSMA6 | 12613 | -0.042 | 0.2 | NO
103 | PSMB6 | PSMB6 | PSMB6 | 12816 | -0.046 | 0.19 | NO
104 | PIK3AP1 | PIK3AP1 | PIK3AP1 | 13039 | -0.051 | 0.18 | NO
105 | PSMD9 | PSMD9 | PSMD9 | 13156 | -0.053 | 0.18 | NO
106 | BAD | BAD | BAD | 13477 | -0.062 | 0.16 | NO
107 | PIK3R1 | PIK3R1 | PIK3R1 | 13802 | -0.071 | 0.15 | NO
108 | PSMA3 | PSMA3 | PSMA3 | 13963 | -0.075 | 0.15 | NO
109 | AKT1S1 | AKT1S1 | AKT1S1 | 14047 | -0.078 | 0.15 | NO
110 | PSMD8 | PSMD8 | PSMD8 | 14124 | -0.08 | 0.15 | NO
111 | PSMC6 | PSMC6 | PSMC6 | 14197 | -0.082 | 0.15 | NO
112 | PSMD14 | PSMD14 | PSMD14 | 14305 | -0.085 | 0.15 | NO
113 | PSMB7 | PSMB7 | PSMB7 | 14330 | -0.086 | 0.16 | NO
114 | PSMC1 | PSMC1 | PSMC1 | 14562 | -0.093 | 0.15 | NO
115 | AKT1 | AKT1 | AKT1 | 14849 | -0.1 | 0.14 | NO
116 | PSMB5 | PSMB5 | PSMB5 | 14932 | -0.11 | 0.14 | NO
117 | SHC1 | SHC1 | SHC1 | 15281 | -0.12 | 0.13 | NO
118 | PHLPP1 | PHLPP1 | PHLPP1 | 15374 | -0.13 | 0.13 | NO
119 | TRIB3 | TRIB3 | TRIB3 | 15553 | -0.14 | 0.13 | NO
120 | CDKN1A | CDKN1A | CDKN1A | 15853 | -0.16 | 0.13 | NO

Figure S41. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION.

Figure S42. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG CHEMOKINE SIGNALING PATHWAY

Table S22. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | IL12B | IL12B | IL12B | 5 | 1.1 | 0.12 | YES
2 | IFNB1 | IFNB1 | IFNB1 | 9 | 1 | 0.23 | YES
3 | TNF | TNF | TNF | 196 | 0.72 | 0.3 | YES
4 | CXCL10 | CXCL10 | CXCL10 | 289 | 0.67 | 0.36 | YES
5 | IL12A | IL12A | IL12A | 608 | 0.54 | 0.4 | YES
6 | MAPK10 | MAPK10 | MAPK10 | 919 | 0.46 | 0.44 | YES
7 | TMEM173 | TMEM173 | TMEM173 | 1927 | 0.31 | 0.42 | YES
8 | RNF125 | RNF125 | RNF125 | 1985 | 0.3 | 0.44 | YES
9 | IKBKE | IKBKE | IKBKE | 2153 | 0.28 | 0.47 | YES
10 | TBKBP1 | TBKBP1 | TBKBP1 | 2338 | 0.26 | 0.48 | YES
11 | CYLD | CYLD | CYLD | 2513 | 0.25 | 0.5 | YES
12 | TRAF3 | TRAF3 | TRAF3 | 3134 | 0.2 | 0.49 | YES
13 | DHX58 | DHX58 | DHX58 | 3403 | 0.18 | 0.49 | YES
14 | CASP8 | CASP8 | CASP8 | 3526 | 0.18 | 0.51 | YES
15 | IFNE | IFNE | IFNE | 3809 | 0.16 | 0.51 | YES
16 | TRIM25 | TRIM25 | TRIM25 | 3886 | 0.16 | 0.52 | YES
17 | IKBKB | IKBKB | IKBKB | 4144 | 0.14 | 0.52 | YES
18 | IFIH1 | IFIH1 | IFIH1 | 4297 | 0.14 | 0.53 | YES
19 | MAP3K1 | MAP3K1 | MAP3K1 | 4349 | 0.14 | 0.54 | YES
20 | TRAF6 | TRAF6 | TRAF6 | 4472 | 0.13 | 0.55 | YES
21 | DDX58 | DDX58 | DDX58 | 4480 | 0.13 | 0.56 | YES
22 | CASP10 | CASP10 | CASP10 | 5038 | 0.11 | 0.54 | NO
23 | TRAF2 | TRAF2 | TRAF2 | 5475 | 0.096 | 0.53 | NO
24 | MAP3K7 | MAP3K7 | MAP3K7 | 5552 | 0.094 | 0.54 | NO
25 | NFKBIA | NFKBIA | NFKBIA | 6092 | 0.081 | 0.52 | NO
26 | ATG12 | ATG12 | ATG12 | 6616 | 0.068 | 0.49 | NO
27 | NFKB1 | NFKB1 | NFKB1 | 6992 | 0.061 | 0.48 | NO
28 | MAVS | MAVS | MAVS | 7031 | 0.06 | 0.48 | NO
29 | MAPK9 | MAPK9 | MAPK9 | 7132 | 0.058 | 0.48 | NO
30 | OTUD5 | OTUD5 | OTUD5 | 7216 | 0.056 | 0.49 | NO
31 | IKBKG | IKBKG | IKBKG | 7261 | 0.055 | 0.49 | NO
32 | ISG15 | ISG15 | ISG15 | 7671 | 0.047 | 0.47 | NO
33 | DDX3X | DDX3X | DDX3X | 7937 | 0.042 | 0.46 | NO
34 | TRADD | TRADD | TRADD | 8046 | 0.04 | 0.46 | NO
35 | TBK1 | TBK1 | TBK1 | 8301 | 0.035 | 0.45 | NO
36 | CHUK | CHUK | CHUK | 8406 | 0.033 | 0.45 | NO
37 | MAPK11 | MAPK11 | MAPK11 | 8426 | 0.033 | 0.45 | NO
38 | MAPK13 | MAPK13 | MAPK13 | 9063 | 0.023 | 0.42 | NO
39 | NFKBIB | NFKBIB | NFKBIB | 9396 | 0.017 | 0.4 | NO
40 | ATG5 | ATG5 | ATG5 | 9593 | 0.014 | 0.39 | NO
41 | IRF3 | IRF3 | IRF3 | 9795 | 0.01 | 0.38 | NO
42 | IRF7 | IRF7 | IRF7 | 9887 | 0.0087 | 0.38 | NO
43 | RELA | RELA | RELA | 10186 | 0.0039 | 0.36 | NO
44 | MAPK14 | MAPK14 | MAPK14 | 10199 | 0.0035 | 0.36 | NO
45 | SIKE1 | SIKE1 | SIKE1 | 10636 | -0.0044 | 0.34 | NO
46 | TANK | TANK | TANK | 10700 | -0.0054 | 0.33 | NO
47 | AZI2 | AZI2 | AZI2 | 11235 | -0.015 | 0.31 | NO
48 | PIN1 | PIN1 | PIN1 | 11435 | -0.019 | 0.3 | NO
49 | FADD | FADD | FADD | 11691 | -0.023 | 0.29 | NO
50 | RIPK1 | RIPK1 | RIPK1 | 12224 | -0.034 | 0.26 | NO
51 | DDX3Y | DDX3Y | DDX3Y | 12425 | -0.038 | 0.25 | NO
52 | MAPK8 | MAPK8 | MAPK8 | 13671 | -0.067 | 0.19 | NO
53 | NLRX1 | NLRX1 | NLRX1 | 14513 | -0.092 | 0.16 | NO
54 | DAK | DAK | DAK | 14642 | -0.096 | 0.16 | NO
55 | IL8 | IL8 | IL8 | 15598 | -0.14 | 0.12 | NO
56 | MAPK12 | MAPK12 | MAPK12 | 16090 | -0.17 | 0.11 | NO

Figure S43. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CHEMOKINE SIGNALING PATHWAY.

Figure S44. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CHEMOKINE SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG ENDOCYTOSIS

Table S23. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | IKZF3 | IKZF3 | IKZF3 | 3 | 1.1 | 0.093 | YES
2 | IFNG | IFNG | IFNG | 46 | 0.9 | 0.17 | YES
3 | PRKCB | PRKCB | PRKCB | 140 | 0.77 | 0.23 | YES
4 | LCK | LCK | LCK | 216 | 0.7 | 0.28 | YES
5 | IL2 | IL2 | IL2 | 228 | 0.7 | 0.34 | YES
6 | IL2RB | IL2RB | IL2RB | 252 | 0.68 | 0.4 | YES
7 | DOK2 | DOK2 | DOK2 | 512 | 0.57 | 0.44 | YES
8 | IL2RA | IL2RA | IL2RA | 614 | 0.54 | 0.48 | YES
9 | BCL2 | BCL2 | BCL2 | 668 | 0.52 | 0.52 | YES
10 | SOCS1 | SOCS1 | SOCS1 | 986 | 0.45 | 0.54 | YES
11 | IL2RG | IL2RG | IL2RG | 1076 | 0.43 | 0.57 | YES
12 | JAK3 | JAK3 | JAK3 | 1122 | 0.42 | 0.6 | YES
13 | STAT5A | STAT5A | STAT5A | 1660 | 0.34 | 0.6 | YES
14 | PTK2B | PTK2B | PTK2B | 1726 | 0.33 | 0.63 | YES
15 | MYC | MYC | MYC | 1917 | 0.31 | 0.64 | YES
16 | SYK | SYK | SYK | 2066 | 0.29 | 0.66 | YES
17 | FYN | FYN | FYN | 2329 | 0.26 | 0.67 | YES
18 | SOCS2 | SOCS2 | SOCS2 | 2981 | 0.21 | 0.65 | NO
19 | GAB2 | GAB2 | GAB2 | 3423 | 0.18 | 0.64 | NO
20 | PRKCE | PRKCE | PRKCE | 4848 | 0.12 | 0.57 | NO
21 | SOCS3 | SOCS3 | SOCS3 | 4920 | 0.12 | 0.58 | NO
22 | SOS1 | SOS1 | SOS1 | 4921 | 0.12 | 0.59 | NO
23 | STAT5B | STAT5B | STAT5B | 5007 | 0.11 | 0.6 | NO
24 | JAK1 | JAK1 | JAK1 | 5307 | 0.1 | 0.59 | NO
25 | STAT1 | STAT1 | STAT1 | 6262 | 0.077 | 0.54 | NO
26 | MAP2K1 | MAP2K1 | MAP2K1 | 7117 | 0.058 | 0.5 | NO
27 | MAPK9 | MAPK9 | MAPK9 | 7132 | 0.058 | 0.5 | NO
28 | GRB2 | GRB2 | GRB2 | 7701 | 0.046 | 0.48 | NO
29 | STAT3 | STAT3 | STAT3 | 7934 | 0.042 | 0.47 | NO
30 | PIK3CA | PIK3CA | PIK3CA | 8332 | 0.035 | 0.45 | NO
31 | MAPK11 | MAPK11 | MAPK11 | 8426 | 0.033 | 0.44 | NO
32 | CISH | CISH | CISH | 8733 | 0.028 | 0.43 | NO
33 | RAF1 | RAF1 | RAF1 | 8847 | 0.026 | 0.43 | NO
34 | MAPK1 | MAPK1 | MAPK1 | 9247 | 0.02 | 0.41 | NO
35 | PPP2R5D | PPP2R5D | PPP2R5D | 9335 | 0.018 | 0.4 | NO
36 | RHOA | RHOA | RHOA | 9637 | 0.013 | 0.39 | NO
37 | MAP2K2 | MAP2K2 | MAP2K2 | 9685 | 0.012 | 0.39 | NO
38 | STAM | STAM | STAM | 9922 | 0.0082 | 0.37 | NO
39 | MAPK14 | MAPK14 | MAPK14 | 10199 | 0.0035 | 0.36 | NO
40 | CDK2 | CDK2 | CDK2 | 10470 | -0.0013 | 0.34 | NO
41 | MAPK3 | MAPK3 | MAPK3 | 11313 | -0.016 | 0.3 | NO
42 | STAM2 | STAM2 | STAM2 | 11317 | -0.016 | 0.3 | NO
43 | KRAS | KRAS | KRAS | 11599 | -0.021 | 0.29 | NO
44 | HRAS | HRAS | HRAS | 11910 | -0.028 | 0.27 | NO
45 | RASA1 | RASA1 | RASA1 | 12005 | -0.03 | 0.27 | NO
46 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 12071 | -0.031 | 0.27 | NO
47 | NRAS | NRAS | NRAS | 12308 | -0.036 | 0.26 | NO
48 | PTPN11 | PTPN11 | PTPN11 | 13114 | -0.052 | 0.22 | NO
49 | JUN | JUN | JUN | 13526 | -0.063 | 0.2 | NO
50 | MAPK8 | MAPK8 | MAPK8 | 13671 | -0.067 | 0.2 | NO
51 | PIK3R1 | PIK3R1 | PIK3R1 | 13802 | -0.071 | 0.2 | NO
52 | FOS | FOS | FOS | 15246 | -0.12 | 0.13 | NO
53 | IRS2 | IRS2 | IRS2 | 15254 | -0.12 | 0.14 | NO
54 | SHC1 | SHC1 | SHC1 | 15281 | -0.12 | 0.15 | NO
55 | IRS1 | IRS1 | IRS1 | 15338 | -0.12 | 0.15 | NO

Figure S45. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ENDOCYTOSIS.

Figure S46. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ENDOCYTOSIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG MTOR SIGNALING PATHWAY

Table S24. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | IFNB1 | IFNB1 | IFNB1 | 9 | 1 | 0.13 | YES
2 | HERC5 | HERC5 | HERC5 | 933 | 0.46 | 0.13 | YES
3 | NLRC5 | NLRC5 | NLRC5 | 1053 | 0.43 | 0.18 | YES
4 | TNFAIP3 | TNFAIP3 | TNFAIP3 | 1676 | 0.34 | 0.19 | YES
5 | S100B | S100B | S100B | 1944 | 0.31 | 0.21 | YES
6 | RNF125 | RNF125 | RNF125 | 1985 | 0.3 | 0.25 | YES
7 | IKBKE | IKBKE | IKBKE | 2153 | 0.28 | 0.27 | YES
8 | IRF1 | IRF1 | IRF1 | 2315 | 0.26 | 0.3 | YES
9 | CYLD | CYLD | CYLD | 2513 | 0.25 | 0.32 | YES
10 | RNF135 | RNF135 | RNF135 | 2675 | 0.23 | 0.34 | YES
11 | UBA7 | UBA7 | UBA7 | 2704 | 0.23 | 0.36 | YES
12 | TRAF3 | TRAF3 | TRAF3 | 3134 | 0.2 | 0.36 | YES
13 | NFKB2 | NFKB2 | NFKB2 | 3315 | 0.19 | 0.38 | YES
14 | DHX58 | DHX58 | DHX58 | 3403 | 0.18 | 0.4 | YES
15 | CASP8 | CASP8 | CASP8 | 3526 | 0.18 | 0.41 | YES
16 | TRIM25 | TRIM25 | TRIM25 | 3886 | 0.16 | 0.41 | YES
17 | AGER | AGER | AGER | 3975 | 0.15 | 0.42 | YES
18 | UBE2L6 | UBE2L6 | UBE2L6 | 4017 | 0.15 | 0.44 | YES
19 | IKBKB | IKBKB | IKBKB | 4144 | 0.14 | 0.45 | YES
20 | IFIH1 | IFIH1 | IFIH1 | 4297 | 0.14 | 0.46 | YES
21 | MAP3K1 | MAP3K1 | MAP3K1 | 4349 | 0.14 | 0.48 | YES
22 | TRAF6 | TRAF6 | TRAF6 | 4472 | 0.13 | 0.48 | YES
23 | DDX58 | DDX58 | DDX58 | 4480 | 0.13 | 0.5 | YES
24 | IRF2 | IRF2 | IRF2 | 4799 | 0.12 | 0.5 | NO
25 | CASP10 | CASP10 | CASP10 | 5038 | 0.11 | 0.5 | NO
26 | TRAF2 | TRAF2 | TRAF2 | 5475 | 0.096 | 0.49 | NO
27 | NFKBIA | NFKBIA | NFKBIA | 6092 | 0.081 | 0.46 | NO
28 | ATG12 | ATG12 | ATG12 | 6616 | 0.068 | 0.44 | NO
29 | RPS27A | RPS27A | RPS27A | 6857 | 0.063 | 0.44 | NO
30 | MAVS | MAVS | MAVS | 7031 | 0.06 | 0.43 | NO
31 | OTUD5 | OTUD5 | OTUD5 | 7216 | 0.056 | 0.43 | NO
32 | IKBKG | IKBKG | IKBKG | 7261 | 0.055 | 0.44 | NO
33 | UBA52 | UBA52 | UBA52 | 7532 | 0.05 | 0.43 | NO
34 | ISG15 | ISG15 | ISG15 | 7671 | 0.047 | 0.42 | NO
35 | TBK1 | TBK1 | TBK1 | 8301 | 0.035 | 0.39 | NO
36 | CREBBP | CREBBP | CREBBP | 8388 | 0.034 | 0.39 | NO
37 | CHUK | CHUK | CHUK | 8406 | 0.033 | 0.4 | NO
38 | UBE2D2 | UBE2D2 | UBE2D2 | 9001 | 0.024 | 0.37 | NO
39 | TAX1BP1 | TAX1BP1 | TAX1BP1 | 9064 | 0.023 | 0.37 | NO
40 | UBE2D3 | UBE2D3 | UBE2D3 | 9300 | 0.019 | 0.36 | NO
41 | NFKBIB | NFKBIB | NFKBIB | 9396 | 0.017 | 0.35 | NO
42 | ATG5 | ATG5 | ATG5 | 9593 | 0.014 | 0.34 | NO
43 | IRF3 | IRF3 | IRF3 | 9795 | 0.01 | 0.33 | NO
44 | IRF7 | IRF7 | IRF7 | 9887 | 0.0087 | 0.33 | NO
45 | EP300 | EP300 | EP300 | 10098 | 0.0051 | 0.32 | NO
46 | RELA | RELA | RELA | 10186 | 0.0039 | 0.31 | NO
47 | PCBP2 | PCBP2 | PCBP2 | 10213 | 0.0033 | 0.31 | NO
48 | SIKE1 | SIKE1 | SIKE1 | 10636 | -0.0044 | 0.29 | NO
49 | TANK | TANK | TANK | 10700 | -0.0054 | 0.29 | NO
50 | HMGB1 | HMGB1 | HMGB1 | 10992 | -0.01 | 0.27 | NO
51 | PIN1 | PIN1 | PIN1 | 11435 | -0.019 | 0.25 | NO
52 | FADD | FADD | FADD | 11691 | -0.023 | 0.24 | NO
53 | UBE2K | UBE2K | UBE2K | 12073 | -0.031 | 0.22 | NO
54 | RIPK1 | RIPK1 | RIPK1 | 12224 | -0.034 | 0.22 | NO
55 | UBE2D1 | UBE2D1 | UBE2D1 | 13124 | -0.052 | 0.18 | NO
56 | NLRX1 | NLRX1 | NLRX1 | 14513 | -0.092 | 0.11 | NO
57 | DAK | DAK | DAK | 14642 | -0.096 | 0.11 | NO
58 | APP | APP | APP | 16221 | -0.18 | 0.05 | NO
59 | S100A12 | S100A12 | S100A12 | 16515 | -0.21 | 0.059 | NO
60 | SAA1 | SAA1 | SAA1 | 16759 | -0.23 | 0.075 | NO

Figure S47. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG MTOR SIGNALING PATHWAY.

Figure S48. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG MTOR SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG APOPTOSIS

Table S25. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | CXCL13 | CXCL13 | CXCL13 | 58 | 0.88 | 0.098 | YES
2 | CXCL11 | CXCL11 | CXCL11 | 137 | 0.77 | 0.18 | YES
3 | CXCL9 | CXCL9 | CXCL9 | 145 | 0.76 | 0.27 | YES
4 | CXCR3 | CXCR3 | CXCR3 | 160 | 0.75 | 0.36 | YES
5 | CXCL10 | CXCL10 | CXCL10 | 289 | 0.67 | 0.43 | YES
6 | ITGAL | ITGAL | ITGAL | 294 | 0.67 | 0.5 | YES
7 | PIK3CD | PIK3CD | PIK3CD | 604 | 0.54 | 0.55 | YES
8 | PF4 | PF4 | PF4 | 977 | 0.45 | 0.58 | YES
9 | ITGB2 | ITGB2 | ITGB2 | 1367 | 0.38 | 0.6 | YES
10 | GNG2 | GNG2 | GNG2 | 1388 | 0.38 | 0.65 | YES
11 | PIK3R3 | PIK3R3 | PIK3R3 | 2404 | 0.26 | 0.62 | NO
12 | ARRB1 | ARRB1 | ARRB1 | 2779 | 0.22 | 0.62 | NO
13 | CCL11 | CCL11 | CCL11 | 3025 | 0.21 | 0.64 | NO
14 | GNAO1 | GNAO1 | GNAO1 | 3326 | 0.19 | 0.64 | NO
15 | GNAZ | GNAZ | GNAZ | 5870 | 0.086 | 0.51 | NO
16 | RICTOR | RICTOR | RICTOR | 6462 | 0.072 | 0.48 | NO
17 | PDPK1 | PDPK1 | PDPK1 | 7024 | 0.06 | 0.46 | NO
18 | MAP2K1 | MAP2K1 | MAP2K1 | 7117 | 0.058 | 0.46 | NO
19 | MTOR | MTOR | MTOR | 7612 | 0.048 | 0.44 | NO
20 | GNAI2 | GNAI2 | GNAI2 | 7880 | 0.043 | 0.43 | NO
21 | PIK3CA | PIK3CA | PIK3CA | 8332 | 0.035 | 0.41 | NO
22 | MAPK11 | MAPK11 | MAPK11 | 8426 | 0.033 | 0.41 | NO
23 | PIK3CB | PIK3CB | PIK3CB | 8488 | 0.032 | 0.41 | NO
24 | RAF1 | RAF1 | RAF1 | 8847 | 0.026 | 0.39 | NO
25 | MAPK1 | MAPK1 | MAPK1 | 9247 | 0.02 | 0.37 | NO
26 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 9409 | 0.017 | 0.37 | NO
27 | MAP2K2 | MAP2K2 | MAP2K2 | 9685 | 0.012 | 0.35 | NO
28 | MAPK14 | MAPK14 | MAPK14 | 10199 | 0.0035 | 0.32 | NO
29 | GNB1 | GNB1 | GNB1 | 10660 | -0.0049 | 0.3 | NO
30 | MAPK3 | MAPK3 | MAPK3 | 11313 | -0.016 | 0.26 | NO
31 | MLST8 | MLST8 | MLST8 | 11392 | -0.018 | 0.26 | NO
32 | KRAS | KRAS | KRAS | 11599 | -0.021 | 0.25 | NO
33 | PIK3R2 | PIK3R2 | PIK3R2 | 11896 | -0.027 | 0.24 | NO
34 | HRAS | HRAS | HRAS | 11910 | -0.028 | 0.24 | NO
35 | NRAS | NRAS | NRAS | 12308 | -0.036 | 0.22 | NO
36 | GNAI3 | GNAI3 | GNAI3 | 12736 | -0.044 | 0.21 | NO
37 | SRC | SRC | SRC | 13184 | -0.054 | 0.19 | NO
38 | PIK3R1 | PIK3R1 | PIK3R1 | 13802 | -0.071 | 0.16 | NO
39 | MAP2K6 | MAP2K6 | MAP2K6 | 14134 | -0.08 | 0.15 | NO
40 | AKT1 | AKT1 | AKT1 | 14849 | -0.1 | 0.13 | NO
41 | DNM1 | DNM1 | DNM1 | 14963 | -0.11 | 0.13 | NO
42 | MAP2K3 | MAP2K3 | MAP2K3 | 15642 | -0.14 | 0.11 | NO
43 | GNAI1 | GNAI1 | GNAI1 | 16616 | -0.22 | 0.083 | NO

Figure S49. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG APOPTOSIS.

Figure S50. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG APOPTOSIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG CELL ADHESION MOLECULES CAMS

Table S26. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | TNF | TNF | TNF | 196 | 0.72 | 0.13 | YES
2 | BCL2 | BCL2 | BCL2 | 668 | 0.52 | 0.2 | YES
3 | BIRC3 | BIRC3 | BIRC3 | 1254 | 0.4 | 0.24 | YES
4 | EGF | EGF | EGF | 1530 | 0.36 | 0.3 | YES
5 | IGF1 | IGF1 | IGF1 | 1615 | 0.35 | 0.36 | YES
6 | MYC | MYC | MYC | 1917 | 0.31 | 0.4 | YES
7 | KSR1 | KSR1 | KSR1 | 2387 | 0.26 | 0.42 | YES
8 | SMPD3 | SMPD3 | SMPD3 | 2910 | 0.21 | 0.43 | YES
9 | CASP8 | CASP8 | CASP8 | 3526 | 0.18 | 0.43 | NO
10 | MAP3K1 | MAP3K1 | MAP3K1 | 4349 | 0.14 | 0.41 | NO
11 | PRKCD | PRKCD | PRKCD | 4661 | 0.12 | 0.42 | NO
12 | NSMAF | NSMAF | NSMAF | 5293 | 0.1 | 0.4 | NO
13 | TRAF2 | TRAF2 | TRAF2 | 5475 | 0.096 | 0.41 | NO
14 | NFKBIA | NFKBIA | NFKBIA | 6092 | 0.081 | 0.39 | NO
15 | BID | BID | BID | 6970 | 0.061 | 0.36 | NO
16 | NFKB1 | NFKB1 | NFKB1 | 6992 | 0.061 | 0.37 | NO
17 | MAP2K1 | MAP2K1 | MAP2K1 | 7117 | 0.058 | 0.37 | NO
18 | PAWR | PAWR | PAWR | 7979 | 0.041 | 0.33 | NO
19 | EIF2A | EIF2A | EIF2A | 8032 | 0.04 | 0.33 | NO
20 | TRADD | TRADD | TRADD | 8046 | 0.04 | 0.34 | NO
21 | EIF2AK2 | EIF2AK2 | EIF2AK2 | 8257 | 0.036 | 0.34 | NO
22 | RAF1 | RAF1 | RAF1 | 8847 | 0.026 | 0.31 | NO
23 | ASAH1 | ASAH1 | ASAH1 | 9150 | 0.022 | 0.3 | NO
24 | MAPK1 | MAPK1 | MAPK1 | 9247 | 0.02 | 0.3 | NO
25 | MAP2K2 | MAP2K2 | MAP2K2 | 9685 | 0.012 | 0.27 | NO
26 | BAG4 | BAG4 | BAG4 | 9888 | 0.0086 | 0.26 | NO
27 | RELA | RELA | RELA | 10186 | 0.0039 | 0.25 | NO
28 | MADD | MADD | MADD | 10305 | 0.0016 | 0.24 | NO
29 | SMPD1 | SMPD1 | SMPD1 | 10315 | 0.0014 | 0.24 | NO
30 | PRKCZ | PRKCZ | PRKCZ | 10771 | -0.0067 | 0.22 | NO
31 | RB1 | RB1 | RB1 | 11082 | -0.012 | 0.2 | NO
32 | PRKRA | PRKRA | PRKRA | 11155 | -0.013 | 0.2 | NO
33 | MAPK3 | MAPK3 | MAPK3 | 11313 | -0.016 | 0.2 | NO
34 | FADD | FADD | FADD | 11691 | -0.023 | 0.18 | NO
35 | MAP2K4 | MAP2K4 | MAP2K4 | 11883 | -0.027 | 0.17 | NO
36 | RIPK1 | RIPK1 | RIPK1 | 12224 | -0.034 | 0.16 | NO
37 | MAP4K4 | MAP4K4 | MAP4K4 | 12410 | -0.038 | 0.16 | NO
38 | SPHK2 | SPHK2 | SPHK2 | 12837 | -0.046 | 0.14 | NO
39 | AIFM1 | AIFM1 | AIFM1 | 13159 | -0.054 | 0.14 | NO
40 | CYCS | CYCS | CYCS | 13458 | -0.061 | 0.13 | NO
41 | BAD | BAD | BAD | 13477 | -0.062 | 0.14 | NO
42 | CTSD | CTSD | CTSD | 13493 | -0.062 | 0.15 | NO
43 | MAPK8 | MAPK8 | MAPK8 | 13671 | -0.067 | 0.16 | NO
44 | BAX | BAX | BAX | 13721 | -0.068 | 0.16 | NO
45 | TNFRSF1A | TNFRSF1A | TNFRSF1A | 14364 | -0.087 | 0.15 | NO
46 | AKT1 | AKT1 | AKT1 | 14849 | -0.1 | 0.14 | NO
47 | PDGFA | PDGFA | PDGFA | 14859 | -0.1 | 0.16 | NO
48 | CRADD | CRADD | CRADD | 15157 | -0.12 | 0.16 | NO

Figure S51. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CELL ADHESION MOLECULES CAMS.

Figure S52. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CELL ADHESION MOLECULES CAMS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG ANTIGEN PROCESSING AND PRESENTATION

Table S27. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | FASLG | FASLG | FASLG | 120 | 0.79 | 0.13 | YES
2 | TNF | TNF | TNF | 196 | 0.72 | 0.25 | YES
3 | CD247 | CD247 | CD247 | 269 | 0.68 | 0.36 | YES
4 | BCL2 | BCL2 | BCL2 | 668 | 0.52 | 0.42 | YES
5 | BIRC3 | BIRC3 | BIRC3 | 1254 | 0.4 | 0.46 | YES
6 | TRAF1 | TRAF1 | TRAF1 | 1648 | 0.34 | 0.5 | YES
7 | MAP3K14 | MAP3K14 | MAP3K14 | 2220 | 0.27 | 0.51 | YES
8 | DFFB | DFFB | DFFB | 2484 | 0.25 | 0.54 | YES
9 | FAS | FAS | FAS | 2573 | 0.24 | 0.57 | YES
10 | MAP3K5 | MAP3K5 | MAP3K5 | 3126 | 0.2 | 0.58 | YES
11 | CASP8 | CASP8 | CASP8 | 3526 | 0.18 | 0.58 | YES
12 | CFLAR | CFLAR | CFLAR | 3841 | 0.16 | 0.6 | YES
13 | TRAF2 | TRAF2 | TRAF2 | 5475 | 0.096 | 0.52 | NO
14 | NFKBIA | NFKBIA | NFKBIA | 6092 | 0.081 | 0.5 | NO
15 | CASP2 | CASP2 | CASP2 | 6208 | 0.078 | 0.51 | NO
16 | BID | BID | BID | 6970 | 0.061 | 0.48 | NO
17 | NFKB1 | NFKB1 | NFKB1 | 6992 | 0.061 | 0.48 | NO
18 | DAXX | DAXX | DAXX | 7097 | 0.058 | 0.49 | NO
19 | DFFA | DFFA | DFFA | 7689 | 0.047 | 0.46 | NO
20 | CASP6 | CASP6 | CASP6 | 7693 | 0.047 | 0.47 | NO
21 | MAP2K7 | MAP2K7 | MAP2K7 | 7959 | 0.041 | 0.46 | NO
22 | CASP3 | CASP3 | CASP3 | 7967 | 0.041 | 0.47 | NO
23 | TRADD | TRADD | TRADD | 8046 | 0.04 | 0.47 | NO
24 | CHUK | CHUK | CHUK | 8406 | 0.033 | 0.46 | NO
25 | BAG4 | BAG4 | BAG4 | 9888 | 0.0086 | 0.38 | NO
26 | RELA | RELA | RELA | 10186 | 0.0039 | 0.36 | NO
27 | APAF1 | APAF1 | APAF1 | 11040 | -0.011 | 0.32 | NO
28 | CASP7 | CASP7 | CASP7 | 11589 | -0.021 | 0.29 | NO
29 | FADD | FADD | FADD | 11691 | -0.023 | 0.29 | NO
30 | CASP9 | CASP9 | CASP9 | 11704 | -0.023 | 0.29 | NO
31 | RIPK1 | RIPK1 | RIPK1 | 12224 | -0.034 | 0.27 | NO
32 | CYCS | CYCS | CYCS | 13458 | -0.061 | 0.21 | NO
33 | MAPK8 | MAPK8 | MAPK8 | 13671 | -0.067 | 0.21 | NO
34 | TNFRSF1A | TNFRSF1A | TNFRSF1A | 14364 | -0.087 | 0.19 | NO
35 | CRADD | CRADD | CRADD | 15157 | -0.12 | 0.16 | NO

Figure S53. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ANTIGEN PROCESSING AND PRESENTATION.

Figure S54. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ANTIGEN PROCESSING AND PRESENTATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY

Table S28. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | IFNG | IFNG | IFNG | 46 | 0.9 | 0.031 | YES
2 | ICOS | ICOS | ICOS | 56 | 0.88 | 0.063 | YES
3 | CD40LG | CD40LG | CD40LG | 81 | 0.84 | 0.093 | YES
4 | CTLA4 | CTLA4 | CTLA4 | 89 | 0.83 | 0.12 | YES
5 | ITK | ITK | ITK | 98 | 0.82 | 0.15 | YES
6 | ZAP70 | ZAP70 | ZAP70 | 153 | 0.76 | 0.18 | YES
7 | CD3E | CD3E | CD3E | 155 | 0.75 | 0.21 | YES
8 | PDCD1 | PDCD1 | PDCD1 | 171 | 0.74 | 0.23 | YES
9 | PIK3CG | PIK3CG | PIK3CG | 174 | 0.74 | 0.26 | YES
10 | CD28 | CD28 | CD28 | 190 | 0.73 | 0.29 | YES
11 | TNF | TNF | TNF | 196 | 0.72 | 0.32 | YES
12 | CD8A | CD8A | CD8A | 215 | 0.7 | 0.34 | YES
13 | LCK | LCK | LCK | 216 | 0.7 | 0.37 | YES
14 | IL2 | IL2 | IL2 | 228 | 0.7 | 0.39 | YES
15 | CD247 | CD247 | CD247 | 269 | 0.68 | 0.42 | YES
16 | PTPRC | PTPRC | PTPRC | 311 | 0.66 | 0.44 | YES
17 | CD8B | CD8B | CD8B | 328 | 0.65 | 0.46 | YES
18 | GRAP2 | GRAP2 | GRAP2 | 338 | 0.65 | 0.48 | YES
19 | IL10 | IL10 | IL10 | 353 | 0.64 | 0.51 | YES
20 | CD3G | CD3G | CD3G | 360 | 0.64 | 0.53 | YES
21 | RASGRP1 | RASGRP1 | RASGRP1 | 366 | 0.63 | 0.56 | YES
22 | CD3D | CD3D | CD3D | 504 | 0.57 | 0.57 | YES
23 | PIK3R5 | PIK3R5 | PIK3R5 | 568 | 0.55 | 0.59 | YES
24 | PIK3CD | PIK3CD | PIK3CD | 604 | 0.54 | 0.6 | YES
25 | VAV1 | VAV1 | VAV1 | 622 | 0.54 | 0.62 | YES
26 | PRKCQ | PRKCQ | PRKCQ | 807 | 0.48 | 0.63 | YES
27 | CARD11 | CARD11 | CARD11 | 991 | 0.44 | 0.64 | YES
28 | LCP2 | LCP2 | LCP2 | 1063 | 0.43 | 0.65 | YES
29 | LAT | LAT | LAT | 1293 | 0.4 | 0.65 | YES
30 | CD4 | CD4 | CD4 | 1566 | 0.35 | 0.65 | YES
31 | MAP3K8 | MAP3K8 | MAP3K8 | 1868 | 0.32 | 0.64 | YES
32 | TEC | TEC | TEC | 1938 | 0.31 | 0.65 | YES
33 | MAP3K14 | MAP3K14 | MAP3K14 | 2220 | 0.27 | 0.65 | YES
34 | NFATC2 | NFATC2 | NFATC2 | 2233 | 0.27 | 0.66 | YES
35 | FYN | FYN | FYN | 2329 | 0.26 | 0.66 | YES
36 | PIK3R3 | PIK3R3 | PIK3R3 | 2404 | 0.26 | 0.67 | YES
37 | NFATC1 | NFATC1 | NFATC1 | 2925 | 0.21 | 0.64 | NO
38 | PTPN6 | PTPN6 | PTPN6 | 3411 | 0.18 | 0.62 | NO
39 | PPP3CC | PPP3CC | PPP3CC | 3686 | 0.17 | 0.62 | NO
40 | IKBKB | IKBKB | IKBKB | 4144 | 0.14 | 0.6 | NO
41 | PDK1 | PDK1 | PDK1 | 4328 | 0.14 | 0.59 | NO
42 | AKT3 | AKT3 | AKT3 | 4602 | 0.13 | 0.58 | NO
43 | SOS1 | SOS1 | SOS1 | 4921 | 0.12 | 0.57 | NO
44 | PLCG1 | PLCG1 | PLCG1 | 5006 | 0.11 | 0.57 | NO
45 | NCK1 | NCK1 | NCK1 | 5080 | 0.11 | 0.57 | NO
46 | BCL10 | BCL10 | BCL10 | 5448 | 0.097 | 0.55 | NO
47 | MAP3K7 | MAP3K7 | MAP3K7 | 5552 | 0.094 | 0.55 | NO
48 | VAV3 | VAV3 | VAV3 | 5867 | 0.086 | 0.53 | NO
49 | CBLB | CBLB | CBLB | 5911 | 0.085 | 0.54 | NO
50 | NFKBIA | NFKBIA | NFKBIA | 6092 | 0.081 | 0.53 | NO
51 | CBL | CBL | CBL | 6102 | 0.081 | 0.53 | NO
52 | MALT1 | MALT1 | MALT1 | 6423 | 0.073 | 0.52 | NO
53 | NFKBIE | NFKBIE | NFKBIE | 6622 | 0.068 | 0.51 | NO
54 | NFATC4 | NFATC4 | NFATC4 | 6734 | 0.066 | 0.5 | NO
55 | NFKB1 | NFKB1 | NFKB1 | 6992 | 0.061 | 0.49 | NO
56 | AKT2 | AKT2 | AKT2 | 7055 | 0.06 | 0.49 | NO
57 | MAP2K1 | MAP2K1 | MAP2K1 | 7117 | 0.058 | 0.49 | NO
58 | MAPK9 | MAPK9 | MAPK9 | 7132 | 0.058 | 0.49 | NO
59 | IKBKG | IKBKG | IKBKG | 7261 | 0.055 | 0.48 | NO
60 | VAV2 | VAV2 | VAV2 | 7674 | 0.047 | 0.46 | NO
61 | GRB2 | GRB2 | GRB2 | 7701 | 0.046 | 0.46 | NO
62 | MAP2K7 | MAP2K7 | MAP2K7 | 7959 | 0.041 | 0.45 | NO
63 | NFATC3 | NFATC3 | NFATC3 | 7964 | 0.041 | 0.45 | NO
64 | GSK3B | GSK3B | GSK3B | 8088 | 0.039 | 0.45 | NO
65 | PIK3CA | PIK3CA | PIK3CA | 8332 | 0.035 | 0.44 | NO
66 | CHUK | CHUK | CHUK | 8406 | 0.033 | 0.43 | NO
67 | MAPK11 | MAPK11 | MAPK11 | 8426 | 0.033 | 0.43 | NO
68 | PIK3CB | PIK3CB | PIK3CB | 8488 | 0.032 | 0.43 | NO
69 | PAK2 | PAK2 | PAK2 | 8657 | 0.03 | 0.42 | NO
70 | RAF1 | RAF1 | RAF1 | 8847 | 0.026 | 0.41 | NO
71 | NFAT5 | NFAT5 | NFAT5 | 9038 | 0.023 | 0.4 | NO
72 | MAPK13 | MAPK13 | MAPK13 | 9063 | 0.023 | 0.4 | NO
73 | PAK7 | PAK7 | PAK7 | 9232 | 0.02 | 0.39 | NO
74 | MAPK1 | MAPK1 | MAPK1 | 9247 | 0.02 | 0.39 | NO
75 | NFKBIB | NFKBIB | NFKBIB | 9396 | 0.017 | 0.39 | NO
76 | RHOA | RHOA | RHOA | 9637 | 0.013 | 0.37 | NO
77 | MAP2K2 | MAP2K2 | MAP2K2 | 9685 | 0.012 | 0.37 | NO
78 | RELA | RELA | RELA | 10186 | 0.0039 | 0.34 | NO
79 | MAPK14 | MAPK14 | MAPK14 | 10199 | 0.0035 | 0.34 | NO
80 | PPP3R1 | PPP3R1 | PPP3R1 | 10704 | -0.0055 | 0.32 | NO
81 | PAK1 | PAK1 | PAK1 | 11171 | -0.013 | 0.29 | NO
82 | MAPK3 | MAPK3 | MAPK3 | 11313 | -0.016 | 0.28 | NO
83 | KRAS | KRAS | KRAS | 11599 | -0.021 | 0.27 | NO
84 | PIK3R2 | PIK3R2 | PIK3R2 | 11896 | -0.027 | 0.25 | NO
85 | HRAS | HRAS | HRAS | 11910 | -0.028 | 0.25 | NO
86 | NRAS | NRAS | NRAS | 12308 | -0.036 | 0.23 | NO
87 | PPP3CB | PPP3CB | PPP3CB | 12472 | -0.039 | 0.22 | NO
88 | PPP3CA | PPP3CA | PPP3CA | 12820 | -0.046 | 0.21 | NO
89 | SOS2 | SOS2 | SOS2 | 12947 | -0.049 | 0.2 | NO
90 | CHP | CHP | CHP | 12995 | -0.05 | 0.2 | NO
91 | JUN | JUN | JUN | 13526 | -0.063 | 0.17 | NO
92 | CDC42 | CDC42 | CDC42 | 13563 | -0.064 | 0.17 | NO
93 | DLG1 | DLG1 | DLG1 | 13651 | -0.066 | 0.17 | NO
94 | PIK3R1 | PIK3R1 | PIK3R1 | 13802 | -0.071 | 0.17 | NO
95 | PAK3 | PAK3 | PAK3 | 13820 | -0.072 | 0.17 | NO
96 | CDK4 | CDK4 | CDK4 | 14110 | -0.08 | 0.16 | NO
97 | NCK2 | NCK2 | NCK2 | 14177 | -0.081 | 0.15 | NO
98 | PAK6 | PAK6 | PAK6 | 14406 | -0.088 | 0.14 | NO
99 | AKT1 | AKT1 | AKT1 | 14849 | -0.1 | 0.12 | NO
100 | FOS | FOS | FOS | 15246 | -0.12 | 0.11 | NO
101 | PAK4 | PAK4 | PAK4 | 15716 | -0.15 | 0.086 | NO
102 | MAPK12 | MAPK12 | MAPK12 | 16090 | -0.17 | 0.072 | NO
103 | CSF2 | CSF2 | CSF2 | 17406 | -0.33 | 0.011 | NO
104 | CBLC | CBLC | CBLC | 17455 | -0.34 | 0.021 | NO
105 | CHP2 | CHP2 | CHP2 | 17725 | -0.42 | 0.022 | NO

Figure S55. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY.

Figure S56. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY

Table S29. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | HERC5 | HERC5 | HERC5 | 933 | 0.46 | 0.064 | YES
2 | NLRC5 | NLRC5 | NLRC5 | 1053 | 0.43 | 0.17 | YES
3 | TNFAIP3 | TNFAIP3 | TNFAIP3 | 1676 | 0.34 | 0.22 | YES
4 | RNF125 | RNF125 | RNF125 | 1985 | 0.3 | 0.28 | YES
5 | IKBKE | IKBKE | IKBKE | 2153 | 0.28 | 0.34 | YES
6 | CYLD | CYLD | CYLD | 2513 | 0.25 | 0.38 | YES
7 | RNF135 | RNF135 | RNF135 | 2675 | 0.23 | 0.43 | YES
8 | UBA7 | UBA7 | UBA7 | 2704 | 0.23 | 0.49 | YES
9 | TRAF3 | TRAF3 | TRAF3 | 3134 | 0.2 | 0.51 | YES
10 | TRIM25 | TRIM25 | TRIM25 | 3886 | 0.16 | 0.51 | YES
11 | UBE2L6 | UBE2L6 | UBE2L6 | 4017 | 0.15 | 0.54 | YES
12 | IFIH1 | IFIH1 | IFIH1 | 4297 | 0.14 | 0.56 | YES
13 | DDX58 | DDX58 | DDX58 | 4480 | 0.13 | 0.58 | YES
14 | ATG12 | ATG12 | ATG12 | 6616 | 0.068 | 0.48 | NO
15 | RPS27A | RPS27A | RPS27A | 6857 | 0.063 | 0.49 | NO
16 | MAVS | MAVS | MAVS | 7031 | 0.06 | 0.49 | NO
17 | OTUD5 | OTUD5 | OTUD5 | 7216 | 0.056 | 0.5 | NO
18 | UBA52 | UBA52 | UBA52 | 7532 | 0.05 | 0.49 | NO
19 | ISG15 | ISG15 | ISG15 | 7671 | 0.047 | 0.5 | NO
20 | TBK1 | TBK1 | TBK1 | 8301 | 0.035 | 0.47 | NO
21 | UBE2D2 | UBE2D2 | UBE2D2 | 9001 | 0.024 | 0.44 | NO
22 | TAX1BP1 | TAX1BP1 | TAX1BP1 | 9064 | 0.023 | 0.44 | NO
23 | UBE2D3 | UBE2D3 | UBE2D3 | 9300 | 0.019 | 0.43 | NO
24 | ATG5 | ATG5 | ATG5 | 9593 | 0.014 | 0.42 | NO
25 | IRF3 | IRF3 | IRF3 | 9795 | 0.01 | 0.41 | NO
26 | PCBP2 | PCBP2 | PCBP2 | 10213 | 0.0033 | 0.39 | NO
27 | PIN1 | PIN1 | PIN1 | 11435 | -0.019 | 0.32 | NO
28 | UBE2K | UBE2K | UBE2K | 12073 | -0.031 | 0.3 | NO
29 | UBE2D1 | UBE2D1 | UBE2D1 | 13124 | -0.052 | 0.25 | NO
30 | NLRX1 | NLRX1 | NLRX1 | 14513 | -0.092 | 0.2 | NO

Figure S57. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY.

Figure S58. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY

Table S30. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | FASLG | FASLG | FASLG | 120 | 0.79 | 0.12 | YES
2 | FAIM2 | FAIM2 | FAIM2 | 271 | 0.68 | 0.22 | YES
3 | BTK | BTK | BTK | 405 | 0.62 | 0.32 | YES
4 | PIK3CD | PIK3CD | PIK3CD | 604 | 0.54 | 0.4 | YES
5 | MAPK10 | MAPK10 | MAPK10 | 919 | 0.46 | 0.45 | YES
6 | BIRC3 | BIRC3 | BIRC3 | 1254 | 0.4 | 0.5 | YES
7 | SYK | SYK | SYK | 2066 | 0.29 | 0.5 | YES
8 | PIK3R3 | PIK3R3 | PIK3R3 | 2404 | 0.26 | 0.53 | YES
9 | FAS | FAS | FAS | 2573 | 0.24 | 0.56 | YES
10 | CASP8 | CASP8 | CASP8 | 3526 | 0.18 | 0.53 | YES
11 | CFLAR | CFLAR | CFLAR | 3841 | 0.16 | 0.54 | YES
12 | IKBKB | IKBKB | IKBKB | 4144 | 0.14 | 0.55 | YES
13 | MAP3K1 | MAP3K1 | MAP3K1 | 4349 | 0.14 | 0.56 | YES
14 | CASP10 | CASP10 | CASP10 | 5038 | 0.11 | 0.54 | NO
15 | RFC1 | RFC1 | RFC1 | 6816 | 0.064 | 0.45 | NO
16 | BID | BID | BID | 6970 | 0.061 | 0.45 | NO
17 | EZR | EZR | EZR | 7012 | 0.06 | 0.46 | NO
18 | PDPK1 | PDPK1 | PDPK1 | 7024 | 0.06 | 0.47 | NO
19 | MAPK9 | MAPK9 | MAPK9 | 7132 | 0.058 | 0.48 | NO
20 | IKBKG | IKBKG | IKBKG | 7261 | 0.055 | 0.48 | NO
21 | MAP2K7 | MAP2K7 | MAP2K7 | 7959 | 0.041 | 0.44 | NO
22 | CASP3 | CASP3 | CASP3 | 7967 | 0.041 | 0.45 | NO
23 | PIK3CA | PIK3CA | PIK3CA | 8332 | 0.035 | 0.44 | NO
24 | CHUK | CHUK | CHUK | 8406 | 0.033 | 0.44 | NO
25 | MAPK11 | MAPK11 | MAPK11 | 8426 | 0.033 | 0.44 | NO
26 | PIK3CB | PIK3CB | PIK3CB | 8488 | 0.032 | 0.44 | NO
27 | MAPK14 | MAPK14 | MAPK14 | 10199 | 0.0035 | 0.35 | NO
28 | SMPD1 | SMPD1 | SMPD1 | 10315 | 0.0014 | 0.34 | NO
29 | FADD | FADD | FADD | 11691 | -0.023 | 0.27 | NO
30 | BIRC2 | BIRC2 | BIRC2 | 11823 | -0.026 | 0.27 | NO
31 | PIK3R2 | PIK3R2 | PIK3R2 | 11896 | -0.027 | 0.27 | NO
32 | RIPK1 | RIPK1 | RIPK1 | 12224 | -0.034 | 0.26 | NO
33 | CLTC | CLTC | CLTC | 12647 | -0.042 | 0.24 | NO
34 | SRC | SRC | SRC | 13184 | -0.054 | 0.22 | NO
35 | MAPK8 | MAPK8 | MAPK8 | 13671 | -0.067 | 0.2 | NO
36 | PIK3R1 | PIK3R1 | PIK3R1 | 13802 | -0.071 | 0.21 | NO
37 | MAP2K6 | MAP2K6 | MAP2K6 | 14134 | -0.08 | 0.2 | NO
38 | AKT1 | AKT1 | AKT1 | 14849 | -0.1 | 0.18 | NO

Figure S59. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY.

Figure S60. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

For the top enriched genes, if you want to check whether they are

- up-regulated, please check the list of up-regulated genes

- down-regulated, please check the list of down-regulated genes

Expression level

For the top enriched genes, if you want to check whether they are

- highly expressed genes, please check the list of high (top 30%) expressed genes

- low expressed genes, please check the list of low (bottom 30%) expressed genes

An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap

Significant gene list

For the top enriched genes, if you want to check whether they are

- significantly differently expressed genes by eBayes lm fit, please check the list of significant genes

Subtype clus4 enriched pathways

Table 6. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus4. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS | 27 | genes.ES.table | 0.68 | 1.4 | 0.14 | 1 | 1 | 0.33 | 0.026 | 0.32 | 1 | 0.95
KEGG GLUTATHIONE METABOLISM | 46 | genes.ES.table | 0.44 | 1.3 | 0.16 | 1 | 1 | 0.22 | 0.077 | 0.2 | 1 | 0.88
KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM | 39 | genes.ES.table | 0.57 | 1.3 | 0.21 | 1 | 1 | 0.23 | 0.026 | 0.22 | 1 | 0.86
KEGG RIBOSOME | 85 | genes.ES.table | 0.49 | 1.2 | 0.36 | 1 | 1 | 0.68 | 0.34 | 0.45 | 1 | 0.86
KEGG SPLICEOSOME | 114 | genes.ES.table | 0.26 | 1.2 | 0.24 | 1 | 1 | 0.37 | 0.26 | 0.27 | 1 | 0.91
KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT | 38 | genes.ES.table | 0.3 | 1.3 | 0.16 | 1 | 1 | 0.26 | 0.16 | 0.22 | 1 | 0.94
BIOCARTA PROTEASOME PATHWAY | 28 | genes.ES.table | 0.44 | 1.2 | 0.25 | 1 | 1 | 1 | 0.56 | 0.44 | 1 | 0.88
REACTOME ER PHAGOSOME PATHWAY | 57 | genes.ES.table | 0.4 | 1.1 | 0.37 | 1 | 1 | 0.51 | 0.31 | 0.35 | 1 | 0.85
REACTOME MEMBRANE TRAFFICKING | 123 | genes.ES.table | 0.25 | 1.2 | 0.28 | 1 | 1 | 0.21 | 0.17 | 0.18 | 1 | 0.9
REACTOME P53 INDEPENDENT G1 S DNA DAMAGE CHECKPOINT | 47 | genes.ES.table | 0.37 | 1.2 | 0.36 | 1 | 1 | 0.38 | 0.22 | 0.3 | 1 | 0.85

genes ES table in pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS

Table S31. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | NQO1 | NQO1 | NQO1 | 408 | 0.37 | 0.091 | YES
2 | ODC1 | ODC1 | ODC1 | 1387 | 0.2 | 0.097 | YES
3 | PSMB2 | PSMB2 | PSMB2 | 2455 | 0.13 | 0.077 | YES
4 | OAZ3 | OAZ3 | OAZ3 | 2576 | 0.12 | 0.11 | YES
5 | PSMB6 | PSMB6 | PSMB6 | 2650 | 0.12 | 0.14 | YES
6 | PSMB9 | PSMB9 | PSMB9 | 2690 | 0.12 | 0.17 | YES
7 | PSMA5 | PSMA5 | PSMA5 | 2955 | 0.1 | 0.19 | YES
8 | PSMB3 | PSMB3 | PSMB3 | 3017 | 0.1 | 0.22 | YES
9 | PSMC4 | PSMC4 | PSMC4 | 3032 | 0.1 | 0.25 | YES
10 | PSMD9 | PSMD9 | PSMD9 | 3077 | 0.1 | 0.28 | YES
11 | PSMB8 | PSMB8 | PSMB8 | 3462 | 0.088 | 0.28 | YES
12 | PSMC5 | PSMC5 | PSMC5 | 3504 | 0.086 | 0.3 | YES
13 | PSMC3 | PSMC3 | PSMC3 | 3582 | 0.084 | 0.33 | YES
14 | PSMB10 | PSMB10 | PSMB10 | 3616 | 0.083 | 0.35 | YES
15 | PSMD4 | PSMD4 | PSMD4 | 3651 | 0.082 | 0.37 | YES
16 | PSMD13 | PSMD13 | PSMD13 | 3753 | 0.078 | 0.39 | YES
17 | PSME2 | PSME2 | PSME2 | 3912 | 0.074 | 0.4 | YES
18 | PSMF1 | PSMF1 | PSMF1 | 4032 | 0.07 | 0.42 | YES
19 | PSMA4 | PSMA4 | PSMA4 | 4525 | 0.057 | 0.41 | YES
20 | PSMB5 | PSMB5 | PSMB5 | 4836 | 0.049 | 0.41 | YES
21 | OAZ1 | OAZ1 | OAZ1 | 5045 | 0.044 | 0.41 | YES
22 | PSMB4 | PSMB4 | PSMB4 | 5068 | 0.044 | 0.42 | YES
23 | PSMA6 | PSMA6 | PSMA6 | 5242 | 0.04 | 0.42 | YES
24 | PSMC1 | PSMC1 | PSMC1 | 5341 | 0.037 | 0.43 | YES
25 | OAZ2 | OAZ2 | OAZ2 | 5997 | 0.022 | 0.4 | NO
26 | PSMD8 | PSMD8 | PSMD8 | 6256 | 0.017 | 0.39 | NO
27 | PSMB7 | PSMB7 | PSMB7 | 6305 | 0.016 | 0.39 | NO
28 | PSME1 | PSME1 | PSME1 | 6498 | 0.011 | 0.39 | NO
29 | PSMA3 | PSMA3 | PSMA3 | 6620 | 0.0083 | 0.38 | NO
30 | PSMA7 | PSMA7 | PSMA7 | 6781 | 0.0049 | 0.38 | NO
31 | PSMD14 | PSMD14 | PSMD14 | 6898 | 0.0023 | 0.37 | NO
32 | PSMD7 | PSMD7 | PSMD7 | 7134 | -0.0025 | 0.36 | NO
33 | PSMA2 | PSMA2 | PSMA2 | 7567 | -0.012 | 0.34 | NO
34 | PSMC6 | PSMC6 | PSMC6 | 7607 | -0.012 | 0.34 | NO
35 | PSMA1 | PSMA1 | PSMA1 | 7708 | -0.015 | 0.34 | NO
36 | PSMB1 | PSMB1 | PSMB1 | 8066 | -0.023 | 0.32 | NO
37 | PSMD1 | PSMD1 | PSMD1 | 8110 | -0.024 | 0.33 | NO
38 | PSMC2 | PSMC2 | PSMC2 | 8243 | -0.027 | 0.33 | NO
39 | PSMD11 | PSMD11 | PSMD11 | 8256 | -0.027 | 0.34 | NO
40 | PSMD12 | PSMD12 | PSMD12 | 8298 | -0.028 | 0.34 | NO
41 | PSMD3 | PSMD3 | PSMD3 | 8649 | -0.036 | 0.34 | NO
42 | PSMD10 | PSMD10 | PSMD10 | 10070 | -0.069 | 0.28 | NO
43 | PSMD6 | PSMD6 | PSMD6 | 10163 | -0.072 | 0.3 | NO
44 | PSME4 | PSME4 | PSME4 | 10314 | -0.075 | 0.31 | NO
45 | PSMD2 | PSMD2 | PSMD2 | 10396 | -0.078 | 0.33 | NO
46 | AZIN1 | AZIN1 | AZIN1 | 12591 | -0.14 | 0.25 | NO
47 | PSMD5 | PSMD5 | PSMD5 | 13390 | -0.18 | 0.26 | NO

Figure S61. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS.

Figure S62. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG GLUTATHIONE METABOLISM

Table S32. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | GTF2H2 | GTF2H2 | GTF2H2 | 1005 | 0.24 | 0.033 | YES
2 | GTF2H2B | GTF2H2B | GTF2H2B | 1209 | 0.22 | 0.1 | YES
3 | POLR2I | POLR2I | POLR2I | 1859 | 0.16 | 0.12 | YES
4 | GTF2H4 | GTF2H4 | GTF2H4 | 2422 | 0.13 | 0.14 | YES
5 | RDBP | RDBP | RDBP | 2529 | 0.12 | 0.18 | YES
6 | POLR2E | POLR2E | POLR2E | 2582 | 0.12 | 0.22 | YES
7 | POLR2C | POLR2C | POLR2C | 3033 | 0.1 | 0.23 | YES
8 | POLR2L | POLR2L | POLR2L | 3344 | 0.091 | 0.25 | YES
9 | CTDP1 | CTDP1 | CTDP1 | 3679 | 0.081 | 0.26 | YES
10 | GTF2F1 | GTF2F1 | GTF2F1 | 3726 | 0.08 | 0.29 | YES
11 | POLR2J | POLR2J | POLR2J | 3782 | 0.078 | 0.31 | YES
12 | SUPT4H1 | SUPT4H1 | SUPT4H1 | 3812 | 0.077 | 0.34 | YES
13 | POLR2G | POLR2G | POLR2G | 3815 | 0.077 | 0.36 | YES
14 | POLR2F | POLR2F | POLR2F | 4817 | 0.05 | 0.33 | NO
15 | SUPT5H | SUPT5H | SUPT5H | 5471 | 0.034 | 0.3 | NO
16 | POLR2K | POLR2K | POLR2K | 5819 | 0.026 | 0.3 | NO
17 | GTF2H1 | GTF2H1 | GTF2H1 | 6037 | 0.021 | 0.29 | NO
18 | TH1L | TH1L | TH1L | 6063 | 0.021 | 0.3 | NO
19 | POLR2H | POLR2H | POLR2H | 6091 | 0.02 | 0.3 | NO
20 | CDK7 | CDK7 | CDK7 | 6603 | 0.0086 | 0.28 | NO
21 | ERCC2 | ERCC2 | ERCC2 | 6696 | 0.0067 | 0.28 | NO
22 | ERCC3 | ERCC3 | ERCC3 | 7282 | -0.0054 | 0.24 | NO
23 | WHSC2 | WHSC2 | WHSC2 | 7499 | -0.01 | 0.24 | NO
24 | GTF2F2 | GTF2F2 | GTF2F2 | 8288 | -0.028 | 0.2 | NO
25 | COBRA1 | COBRA1 | COBRA1 | 8659 | -0.036 | 0.2 | NO
26 | POLR2A | POLR2A | POLR2A | 8701 | -0.037 | 0.21 | NO
27 | NCBP2 | NCBP2 | NCBP2 | 8840 | -0.041 | 0.22 | NO
28 | CCNH | CCNH | CCNH | 9146 | -0.048 | 0.22 | NO
29 | POLR2D | POLR2D | POLR2D | 10029 | -0.068 | 0.19 | NO
30 | POLR2B | POLR2B | POLR2B | 11370 | -0.1 | 0.16 | NO
31 | NCBP1 | NCBP1 | NCBP1 | 12851 | -0.15 | 0.13 | NO
32 | MNAT1 | MNAT1 | MNAT1 | 13964 | -0.21 | 0.14 | NO
33 | GTF2H3 | GTF2H3 | GTF2H3 | 14445 | -0.23 | 0.2 | NO

Figure S63. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLUTATHIONE METABOLISM.

Figure S64. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLUTATHIONE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM

Table S33. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | UGT1A9 | UGT1A9 | UGT1A9 | 84 | 0.59 | 0.092 | YES
2 | UGT2B11 | UGT2B11 | UGT2B11 | 133 | 0.52 | 0.18 | YES
3 | UGT1A8 | UGT1A8 | UGT1A8 | 136 | 0.52 | 0.26 | YES
4 | UGT1A6 | UGT1A6 | UGT1A6 | 139 | 0.52 | 0.35 | YES
5 | UGT1A10 | UGT1A10 | UGT1A10 | 175 | 0.49 | 0.42 | YES
6 | UGT1A7 | UGT1A7 | UGT1A7 | 197 | 0.48 | 0.5 | YES
7 | UGT2B28 | UGT2B28 | UGT2B28 | 266 | 0.44 | 0.57 | YES
8 | UGT1A5 | UGT1A5 | UGT1A5 | 308 | 0.41 | 0.64 | YES
9 | UGT2B4 | UGT2B4 | UGT2B4 | 476 | 0.35 | 0.68 | YES
10 | UGT2A1 | UGT2A1 | UGT2A1 | 2875 | 0.11 | 0.57 | NO
11 | UGT2B15 | UGT2B15 | UGT2B15 | 2928 | 0.1 | 0.58 | NO
12 | UGDH | UGDH | UGDH | 6107 | 0.02 | 0.41 | NO
13 | GUSB | GUSB | GUSB | 6524 | 0.01 | 0.39 | NO
14 | XYLB | XYLB | XYLB | 6672 | 0.0072 | 0.38 | NO
15 | DCXR | DCXR | DCXR | 10586 | -0.082 | 0.18 | NO
16 | RPE | RPE | RPE | 10728 | -0.086 | 0.18 | NO
17 | AKR1B1 | AKR1B1 | AKR1B1 | 10818 | -0.089 | 0.2 | NO
18 | UGT2B7 | UGT2B7 | UGT2B7 | 10886 | -0.09 | 0.21 | NO
19 | UGT1A3 | UGT1A3 | UGT1A3 | 11432 | -0.11 | 0.19 | NO
20 | DHDH | DHDH | DHDH | 11547 | -0.11 | 0.2 | NO
21 | UGP2 | UGP2 | UGP2 | 11576 | -0.11 | 0.22 | NO
22 | UGT1A1 | UGT1A1 | UGT1A1 | 11652 | -0.11 | 0.24 | NO
23 | UGT2A3 | UGT2A3 | UGT2A3 | 11820 | -0.12 | 0.24 | NO
24 | LOC729020 | LOC729020 | LOC729020 | 12479 | -0.14 | 0.23 | NO
25 | UGT2B10 | UGT2B10 | UGT2B10 | 12717 | -0.15 | 0.24 | NO
26 | UGT1A4 | UGT1A4 | UGT1A4 | 12816 | -0.15 | 0.26 | NO
27 | CRYL1 | CRYL1 | CRYL1 | 13497 | -0.18 | 0.26 | NO

Figure S65. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM.

Figure S66. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG RIBOSOME

Table S34. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | VPS37D | VPS37D | VPS37D | 403 | 0.37 | 0.15 | YES
2 | SNF8 | SNF8 | SNF8 | 1756 | 0.17 | 0.15 | YES
3 | CHMP6 | CHMP6 | CHMP6 | 2018 | 0.15 | 0.21 | YES
4 | CHMP2A | CHMP2A | CHMP2A | 2366 | 0.13 | 0.25 | YES
5 | CHMP4A | CHMP4A | CHMP4A | 3120 | 0.098 | 0.25 | YES
6 | UBA52 | UBA52 | UBA52 | 3125 | 0.098 | 0.3 | YES
7 | CHMP4B | CHMP4B | CHMP4B | 4016 | 0.071 | 0.28 | YES
8 | VPS25 | VPS25 | VPS25 | 4079 | 0.069 | 0.31 | YES
9 | VPS37C | VPS37C | VPS37C | 4663 | 0.054 | 0.3 | YES
10 | TSG101 | TSG101 | TSG101 | 4673 | 0.054 | 0.33 | YES
11 | VPS28 | VPS28 | VPS28 | 4717 | 0.052 | 0.35 | YES
12 | HGS | HGS | HGS | 4908 | 0.048 | 0.36 | YES
13 | RPS27A | RPS27A | RPS27A | 5515 | 0.033 | 0.34 | NO
14 | VPS4A | VPS4A | VPS4A | 5845 | 0.026 | 0.34 | NO
15 | CHMP7 | CHMP7 | CHMP7 | 6103 | 0.02 | 0.33 | NO
16 | CHMP4C | CHMP4C | CHMP4C | 7692 | -0.014 | 0.25 | NO
17 | VPS37B | VPS37B | VPS37B | 8244 | -0.027 | 0.23 | NO
18 | VPS4B | VPS4B | VPS4B | 8349 | -0.029 | 0.24 | NO
19 | VPS36 | VPS36 | VPS36 | 8801 | -0.04 | 0.23 | NO
20 | STAM2 | STAM2 | STAM2 | 10098 | -0.07 | 0.19 | NO
21 | VPS37A | VPS37A | VPS37A | 10585 | -0.082 | 0.2 | NO
22 | STAM | STAM | STAM | 10835 | -0.089 | 0.23 | NO
23 | CHMP5 | CHMP5 | CHMP5 | 11785 | -0.12 | 0.23 | NO
24 | VTA1 | VTA1 | VTA1 | 12041 | -0.12 | 0.28 | NO
25 | CHMP2B | CHMP2B | CHMP2B | 12235 | -0.13 | 0.32 | NO

Figure S67. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG RIBOSOME.

Figure S68. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RIBOSOME, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG SPLICEOSOME

Table S35. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | SNAP25 | SNAP25 | SNAP25 | 712 | 0.29 | 0.036 | YES
2 | USE1 | USE1 | USE1 | 1070 | 0.23 | 0.076 | YES
3 | VAMP5 | VAMP5 | VAMP5 | 1229 | 0.22 | 0.12 | YES
4 | STX1A | STX1A | STX1A | 1379 | 0.2 | 0.17 | YES
5 | STX3 | STX3 | STX3 | 1568 | 0.18 | 0.2 | YES
6 | STX1B | STX1B | STX1B | 1902 | 0.16 | 0.22 | YES
7 | BNIP1 | BNIP1 | BNIP1 | 2120 | 0.14 | 0.25 | YES
8 | VAMP8 | VAMP8 | VAMP8 | 2320 | 0.13 | 0.27 | YES
9 | STX8 | STX8 | STX8 | 2569 | 0.12 | 0.29 | YES
10 | STX10 | STX10 | STX10 | 2870 | 0.11 | 0.3 | YES
11 | STX4 | STX4 | STX4 | 3603 | 0.084 | 0.28 | NO
12 | VTI1B | VTI1B | VTI1B | 4154 | 0.067 | 0.27 | NO
13 | STX5 | STX5 | STX5 | 4560 | 0.056 | 0.26 | NO
14 | BET1L | BET1L | BET1L | 5564 | 0.032 | 0.22 | NO
15 | YKT6 | YKT6 | YKT6 | 5637 | 0.03 | 0.22 | NO
16 | SEC22B | SEC22B | SEC22B | 6420 | 0.013 | 0.18 | NO
17 | SNAP29 | SNAP29 | SNAP29 | 6526 | 0.01 | 0.18 | NO
18 | STX18 | STX18 | STX18 | 7096 | -0.0018 | 0.14 | NO
19 | STX2 | STX2 | STX2 | 8418 | -0.031 | 0.08 | NO
20 | VAMP3 | VAMP3 | VAMP3 | 8466 | -0.032 | 0.086 | NO
21 | STX7 | STX7 | STX7 | 8581 | -0.035 | 0.088 | NO
22 | VTI1A | VTI1A | VTI1A | 8695 | -0.037 | 0.092 | NO
23 | STX16 | STX16 | STX16 | 8962 | -0.043 | 0.088 | NO
24 | GOSR2 | GOSR2 | GOSR2 | 9305 | -0.051 | 0.083 | NO
25 | VAMP4 | VAMP4 | VAMP4 | 9702 | -0.06 | 0.076 | NO
26 | TSNARE1 | TSNARE1 | TSNARE1 | 9748 | -0.062 | 0.09 | NO
27 | GOSR1 | GOSR1 | GOSR1 | 9997 | -0.068 | 0.094 | NO
28 | SNAP47 | SNAP47 | SNAP47 | 10319 | -0.075 | 0.095 | NO
29 | STX12 | STX12 | STX12 | 10513 | -0.08 | 0.1 | NO
30 | SNAP23 | SNAP23 | SNAP23 | 10515 | -0.08 | 0.13 | NO
31 | BET1 | BET1 | BET1 | 10712 | -0.086 | 0.14 | NO
32 | VAMP2 | VAMP2 | VAMP2 | 10779 | -0.088 | 0.16 | NO
33 | STX6 | STX6 | STX6 | 10848 | -0.089 | 0.18 | NO
34 | VAMP7 | VAMP7 | VAMP7 | 10894 | -0.091 | 0.2 | NO
35 | STX17 | STX17 | STX17 | 11310 | -0.1 | 0.2 | NO
36 | STX19 | STX19 | STX19 | 12501 | -0.14 | 0.17 | NO
37 | VAMP1 | VAMP1 | VAMP1 | 13743 | -0.19 | 0.15 | NO
38 | STX11 | STX11 | STX11 | 16029 | -0.35 | 0.12 | NO

Figure S69. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG SPLICEOSOME.

Figure S70. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG SPLICEOSOME, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT

Table S36. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | LSM2 | LSM2 | LSM2 | 1735 | 0.17 | -0.03 | YES
2 | POLR2I | POLR2I | POLR2I | 1859 | 0.16 | 0.025 | YES
3 | TXNL4A | TXNL4A | TXNL4A | 2332 | 0.13 | 0.05 | YES
4 | POLR2E | POLR2E | POLR2E | 2582 | 0.12 | 0.083 | YES
5 | POLR2C | POLR2C | POLR2C | 3033 | 0.1 | 0.098 | YES
6 | SF3B4 | SF3B4 | SF3B4 | 3139 | 0.098 | 0.13 | YES
7 | SNRPB | SNRPB | SNRPB | 3160 | 0.097 | 0.17 | YES
8 | SNRPD2 | SNRPD2 | SNRPD2 | 3334 | 0.092 | 0.19 | YES
9 | POLR2L | POLR2L | POLR2L | 3344 | 0.091 | 0.23 | YES
10 | GTF2F1 | GTF2F1 | GTF2F1 | 3726 | 0.08 | 0.24 | YES
11 | POLR2J | POLR2J | POLR2J | 3782 | 0.078 | 0.26 | YES
12 | SNRPD1 | SNRPD1 | SNRPD1 | 3807 | 0.077 | 0.29 | YES
13 | POLR2G | POLR2G | POLR2G | 3815 | 0.077 | 0.32 | YES
14 | SNRPG | SNRPG | SNRPG | 3832 | 0.076 | 0.35 | YES
15 | SNRPF | SNRPF | SNRPF | 3911 | 0.074 | 0.38 | YES
16 | PRPF6 | PRPF6 | PRPF6 | 3969 | 0.072 | 0.4 | YES
17 | SNRPE | SNRPE | SNRPE | 4708 | 0.053 | 0.38 | YES
18 | SNRPD3 | SNRPD3 | SNRPD3 | 4741 | 0.052 | 0.4 | YES
19 | POLR2F | POLR2F | POLR2F | 4817 | 0.05 | 0.41 | YES
20 | DDX23 | DDX23 | DDX23 | 5296 | 0.038 | 0.4 | NO
21 | SF3B5 | SF3B5 | SF3B5 | 5712 | 0.029 | 0.39 | NO
22 | POLR2K | POLR2K | POLR2K | 5819 | 0.026 | 0.39 | NO
23 | SF3B2 | SF3B2 | SF3B2 | 5981 | 0.023 | 0.39 | NO
24 | POLR2H | POLR2H | POLR2H | 6091 | 0.02 | 0.4 | NO
25 | NHP2L1 | NHP2L1 | NHP2L1 | 6191 | 0.018 | 0.4 | NO
26 | SNRNP40 | SNRNP40 | SNRNP40 | 6330 | 0.015 | 0.4 | NO
27 | SF3B14 | SF3B14 | SF3B14 | 6519 | 0.01 | 0.39 | NO
28 | SF3B3 | SF3B3 | SF3B3 | 7043 | -0.0007 | 0.36 | NO
29 | EFTUD2 | EFTUD2 | EFTUD2 | 8275 | -0.028 | 0.3 | NO
30 | GTF2F2 | GTF2F2 | GTF2F2 | 8288 | -0.028 | 0.31 | NO
31 | POLR2A | POLR2A | POLR2A | 8701 | -0.037 | 0.3 | NO
32 | SNRNP200 | SNRNP200 | SNRNP200 | 8741 | -0.038 | 0.32 | NO
33 | NCBP2 | NCBP2 | NCBP2 | 8840 | -0.041 | 0.33 | NO
34 | POLR2D | POLR2D | POLR2D | 10029 | -0.068 | 0.29 | NO
35 | PRPF8 | PRPF8 | PRPF8 | 10034 | -0.068 | 0.32 | NO
36 | SF3B1 | SF3B1 | SF3B1 | 10509 | -0.08 | 0.32 | NO
37 | POLR2B | POLR2B | POLR2B | 11370 | -0.1 | 0.31 | NO
38 | NCBP1 | NCBP1 | NCBP1 | 12851 | -0.15 | 0.29 | NO

Figure S71. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT.

Figure S72. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA PROTEASOME PATHWAY

Table S37. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | GMNN | GMNN | GMNN | 1854 | 0.16 | -0.046 | YES
2 | PSMB2 | PSMB2 | PSMB2 | 2455 | 0.13 | -0.035 | YES
3 | PSMB6 | PSMB6 | PSMB6 | 2650 | 0.12 | -0.005 | YES
4 | PSMB9 | PSMB9 | PSMB9 | 2690 | 0.12 | 0.033 | YES
5 | PSMA5 | PSMA5 | PSMA5 | 2955 | 0.1 | 0.055 | YES
6 | PSMB3 | PSMB3 | PSMB3 | 3017 | 0.1 | 0.088 | YES
7 | PSMC4 | PSMC4 | PSMC4 | 3032 | 0.1 | 0.12 | YES
8 | PSMD9 | PSMD9 | PSMD9 | 3077 | 0.1 | 0.16 | YES
9 | UBA52 | UBA52 | UBA52 | 3125 | 0.098 | 0.19 | YES
10 | CDT1 | CDT1 | CDT1 | 3379 | 0.09 | 0.2 | YES
11 | PSMB8 | PSMB8 | PSMB8 | 3462 | 0.088 | 0.23 | YES
12 | PSMC5 | PSMC5 | PSMC5 | 3504 | 0.086 | 0.26 | YES
13 | PSMC3 | PSMC3 | PSMC3 | 3582 | 0.084 | 0.28 | YES
14 | PSMB10 | PSMB10 | PSMB10 | 3616 | 0.083 | 0.31 | YES
15 | PSMD4 | PSMD4 | PSMD4 | 3651 | 0.082 | 0.34 | YES
16 | PSMD13 | PSMD13 | PSMD13 | 3753 | 0.078 | 0.36 | YES
17 | PSME2 | PSME2 | PSME2 | 3912 | 0.074 | 0.38 | YES
18 | PSMF1 | PSMF1 | PSMF1 | 4032 | 0.07 | 0.4 | YES
19 | MCM8 | MCM8 | MCM8 | 4086 | 0.069 | 0.42 | YES
20 | PSMA4 | PSMA4 | PSMA4 | 4525 | 0.057 | 0.41 | YES
21 | PSMB5 | PSMB5 | PSMB5 | 4836 | 0.049 | 0.41 | YES
22 | PSMB4 | PSMB4 | PSMB4 | 5068 | 0.044 | 0.41 | YES
23 | PSMA6 | PSMA6 | PSMA6 | 5242 | 0.04 | 0.42 | YES
24 | PSMC1 | PSMC1 | PSMC1 | 5341 | 0.037 | 0.43 | YES
25 | RPS27A | RPS27A | RPS27A | 5515 | 0.033 | 0.43 | YES
26 | CDC6 | CDC6 | CDC6 | 5772 | 0.027 | 0.42 | NO
27 | PSMD8 | PSMD8 | PSMD8 | 6256 | 0.017 | 0.4 | NO
28 | PSMB7 | PSMB7 | PSMB7 | 6305 | 0.016 | 0.4 | NO
29 | PSME1 | PSME1 | PSME1 | 6498 | 0.011 | 0.4 | NO
30 | PSMA3 | PSMA3 | PSMA3 | 6620 | 0.0083 | 0.4 | NO
31 | PSMA7 | PSMA7 | PSMA7 | 6781 | 0.0049 | 0.39 | NO
32 | PSMD14 | PSMD14 | PSMD14 | 6898 | 0.0023 | 0.38 | NO
33 | PSMD7 | PSMD7 | PSMD7 | 7134 | -0.0025 | 0.37 | NO
34 | PSMA2 | PSMA2 | PSMA2 | 7567 | -0.012 | 0.35 | NO
35 | PSMC6 | PSMC6 | PSMC6 | 7607 | -0.012 | 0.35 | NO
36 | PSMA1 | PSMA1 | PSMA1 | 7708 | -0.015 | 0.35 | NO
37 | PSMB1 | PSMB1 | PSMB1 | 8066 | -0.023 | 0.34 | NO
38 | PSMD1 | PSMD1 | PSMD1 | 8110 | -0.024 | 0.35 | NO
39 | PSMC2 | PSMC2 | PSMC2 | 8243 | -0.027 | 0.35 | NO
40 | PSMD11 | PSMD11 | PSMD11 | 8256 | -0.027 | 0.36 | NO
41 | PSMD12 | PSMD12 | PSMD12 | 8298 | -0.028 | 0.36 | NO
42 | PSMD3 | PSMD3 | PSMD3 | 8649 | -0.036 | 0.36 | NO
43 | PSMD10 | PSMD10 | PSMD10 | 10070 | -0.069 | 0.3 | NO
44 | PSMD6 | PSMD6 | PSMD6 | 10163 | -0.072 | 0.32 | NO
45 | PSME4 | PSME4 | PSME4 | 10314 | -0.075 | 0.34 | NO
46 | PSMD2 | PSMD2 | PSMD2 | 10396 | -0.078 | 0.36 | NO
47 | PSMD5 | PSMD5 | PSMD5 | 13390 | -0.18 | 0.26 | NO

Figure S73. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA PROTEASOME PATHWAY.

Figure S74. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PROTEASOME PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME ER PHAGOSOME PATHWAY

Table S38. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | GGT1 | GGT1 | GGT1 | 259 | 0.44 | 0.064 | YES
2 | GPX2 | GPX2 | GPX2 | 393 | 0.38 | 0.12 | YES
3 | GSTO2 | GSTO2 | GSTO2 | 451 | 0.36 | 0.18 | YES
4 | ANPEP | ANPEP | ANPEP | 570 | 0.32 | 0.23 | YES
5 | GSTM2 | GSTM2 | GSTM2 | 865 | 0.26 | 0.26 | YES
6 | GSTP1 | GSTP1 | GSTP1 | 875 | 0.26 | 0.31 | YES
7 | GSTT1 | GSTT1 | GSTT1 | 918 | 0.26 | 0.35 | YES
8 | G6PD | G6PD | G6PD | 1095 | 0.23 | 0.38 | YES
9 | GPX4 | GPX4 | GPX4 | 1291 | 0.21 | 0.41 | YES
10 | ODC1 | ODC1 | ODC1 | 1387 | 0.2 | 0.44 | YES
11 | GSTM4 | GSTM4 | GSTM4 | 2166 | 0.14 | 0.42 | NO
12 | GSTZ1 | GSTZ1 | GSTZ1 | 2658 | 0.12 | 0.41 | NO
13 | GSTM1 | GSTM1 | GSTM1 | 2846 | 0.11 | 0.42 | NO
14 | GSTO1 | GSTO1 | GSTO1 | 3106 | 0.099 | 0.42 | NO
15 | GSTA1 | GSTA1 | GSTA1 | 3721 | 0.08 | 0.4 | NO
16 | GCLM | GCLM | GCLM | 4254 | 0.065 | 0.39 | NO
17 | TXNDC12 | TXNDC12 | TXNDC12 | 4736 | 0.052 | 0.37 | NO
18 | GPX1 | GPX1 | GPX1 | 4865 | 0.049 | 0.37 | NO
19 | OPLAH | OPLAH | OPLAH | 5012 | 0.045 | 0.37 | NO
20 | MGST3 | MGST3 | MGST3 | 5393 | 0.036 | 0.36 | NO
21 | GSS | GSS | GSS | 5520 | 0.033 | 0.35 | NO
22 | PGD | PGD | PGD | 5657 | 0.03 | 0.35 | NO
23 | GSTM3 | GSTM3 | GSTM3 | 5879 | 0.025 | 0.34 | NO
24 | GPX7 | GPX7 | GPX7 | 6261 | 0.016 | 0.33 | NO
25 | SRM | SRM | SRM | 6435 | 0.012 | 0.32 | NO
26 | GSTA2 | GSTA2 | GSTA2 | 6785 | 0.0048 | 0.3 | NO
27 | IDH1 | IDH1 | IDH1 | 6832 | 0.0038 | 0.3 | NO
28 | MGST2 | MGST2 | MGST2 | 6891 | 0.0024 | 0.3 | NO
29 | IDH2 | IDH2 | IDH2 | 7165 | -0.0034 | 0.28 | NO
30 | GSR | GSR | GSR | 7408 | -0.0082 | 0.27 | NO
31 | GSTK1 | GSTK1 | GSTK1 | 7483 | -0.0099 | 0.27 | NO
32 | GCLC | GCLC | GCLC | 7970 | -0.021 | 0.24 | NO
33 | RRM2 | RRM2 | RRM2 | 8531 | -0.034 | 0.22 | NO
34 | MGST1 | MGST1 | MGST1 | 8858 | -0.041 | 0.21 | NO
35 | GSTA4 | GSTA4 | GSTA4 | 8970 | -0.044 | 0.21 | NO
36 | GGCT | GGCT | GGCT | 9248 | -0.05 | 0.2 | NO
37 | RRM1 | RRM1 | RRM1 | 9366 | -0.052 | 0.2 | NO
38 | RRM2B | RRM2B | RRM2B | 9557 | -0.057 | 0.2 | NO
39 | SMS | SMS | SMS | 9841 | -0.064 | 0.2 | NO
40 | GPX3 | GPX3 | GPX3 | 9983 | -0.067 | 0.2 | NO
41 | LAP3 | LAP3 | LAP3 | 11427 | -0.11 | 0.14 | NO
42 | GGT5 | GGT5 | GGT5 | 13055 | -0.16 | 0.082 | NO
43 | GGT7 | GGT7 | GGT7 | 13077 | -0.16 | 0.11 | NO
44 | GSTM5 | GSTM5 | GSTM5 | 14091 | -0.22 | 0.091 | NO
45 | GSTT2 | GSTT2 | GSTT2 | 16070 | -0.35 | 0.043 | NO
46 | GGT6 | GGT6 | GGT6 | 16529 | -0.4 | 0.088 | NO

Figure S75. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME ER PHAGOSOME PATHWAY.

Figure S76. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ER PHAGOSOME PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME MEMBRANE TRAFFICKING

Table S39. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | UGT1A9 | UGT1A9 | UGT1A9 | 84 | 0.59 | 0.076 | YES
2 | UGT2B11 | UGT2B11 | UGT2B11 | 133 | 0.52 | 0.15 | YES
3 | UGT1A8 | UGT1A8 | UGT1A8 | 136 | 0.52 | 0.22 | YES
4 | UGT1A6 | UGT1A6 | UGT1A6 | 139 | 0.52 | 0.29 | YES
5 | UGT1A10 | UGT1A10 | UGT1A10 | 175 | 0.49 | 0.36 | YES
6 | UGT1A7 | UGT1A7 | UGT1A7 | 197 | 0.48 | 0.42 | YES
7 | UGT2B28 | UGT2B28 | UGT2B28 | 266 | 0.44 | 0.48 | YES
8 | UGT1A5 | UGT1A5 | UGT1A5 | 308 | 0.41 | 0.53 | YES
9 | UGT2B4 | UGT2B4 | UGT2B4 | 476 | 0.35 | 0.57 | YES
10 | FTH1 | FTH1 | FTH1 | 2132 | 0.14 | 0.5 | NO
11 | UROD | UROD | UROD | 2852 | 0.11 | 0.47 | NO
12 | UGT2A1 | UGT2A1 | UGT2A1 | 2875 | 0.11 | 0.49 | NO
13 | UGT2B15 | UGT2B15 | UGT2B15 | 2928 | 0.1 | 0.5 | NO
14 | PPOX | PPOX | PPOX | 2997 | 0.1 | 0.51 | NO
15 | ALAS2 | ALAS2 | ALAS2 | 3187 | 0.096 | 0.51 | NO
16 | HMOX1 | HMOX1 | HMOX1 | 3417 | 0.089 | 0.51 | NO
17 | HMBS | HMBS | HMBS | 3746 | 0.079 | 0.5 | NO
18 | BLVRB | BLVRB | BLVRB | 4180 | 0.066 | 0.49 | NO
19 | MMAB | MMAB | MMAB | 5364 | 0.037 | 0.43 | NO
20 | COX10 | COX10 | COX10 | 5830 | 0.026 | 0.41 | NO
21 | FECH | FECH | FECH | 6126 | 0.02 | 0.39 | NO
22 | COX15 | COX15 | COX15 | 6463 | 0.012 | 0.38 | NO
23 | GUSB | GUSB | GUSB | 6524 | 0.01 | 0.37 | NO
24 | EARS2 | EARS2 | EARS2 | 6814 | 0.0041 | 0.36 | NO
25 | HMOX2 | HMOX2 | HMOX2 | 7399 | -0.008 | 0.33 | NO
26 | UROS | UROS | UROS | 7495 | -0.01 | 0.32 | NO
27 | HCCS | HCCS | HCCS | 9825 | -0.064 | 0.2 | NO
28 | BLVRA | BLVRA | BLVRA | 10198 | -0.073 | 0.19 | NO
29 | ALAS1 | ALAS1 | ALAS1 | 10313 | -0.075 | 0.2 | NO
30 | UGT2B7 | UGT2B7 | UGT2B7 | 10886 | -0.09 | 0.18 | NO
31 | ALAD | ALAD | ALAD | 11032 | -0.094 | 0.18 | NO
32 | EPRS | EPRS | EPRS | 11413 | -0.1 | 0.18 | NO
33 | UGT1A3 | UGT1A3 | UGT1A3 | 11432 | -0.11 | 0.19 | NO
34 | UGT1A1 | UGT1A1 | UGT1A1 | 11652 | -0.11 | 0.19 | NO
35 | UGT2A3 | UGT2A3 | UGT2A3 | 11820 | -0.12 | 0.2 | NO
36 | UGT2B10 | UGT2B10 | UGT2B10 | 12717 | -0.15 | 0.17 | NO
37 | UGT1A4 | UGT1A4 | UGT1A4 | 12816 | -0.15 | 0.19 | NO
38 | CPOX | CPOX | CPOX | 14566 | -0.24 | 0.12 | NO
39 | CP | CP | CP | 17409 | -0.53 | 0.039 | NO

Figure S77. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME MEMBRANE TRAFFICKING.

Figure S78. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME MEMBRANE TRAFFICKING, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME P53 INDEPENDENT G1 S DNA DAMAGE CHECKPOINT

Table S40. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | APOBEC3G | APOBEC3G | APOBEC3G | 1622 | 0.18 | -0.029 | YES
2 | PSMB2 | PSMB2 | PSMB2 | 2455 | 0.13 | -0.031 | YES
3 | PSMB6 | PSMB6 | PSMB6 | 2650 | 0.12 | -0.0015 | YES
4 | PSMB9 | PSMB9 | PSMB9 | 2690 | 0.12 | 0.036 | YES
5 | PSMA5 | PSMA5 | PSMA5 | 2955 | 0.1 | 0.058 | YES
6 | PSMB3 | PSMB3 | PSMB3 | 3017 | 0.1 | 0.089 | YES
7 | PSMC4 | PSMC4 | PSMC4 | 3032 | 0.1 | 0.12 | YES
8 | PSMD9 | PSMD9 | PSMD9 | 3077 | 0.1 | 0.16 | YES
9 | UBA52 | UBA52 | UBA52 | 3125 | 0.098 | 0.19 | YES
10 | TCEB2 | TCEB2 | TCEB2 | 3316 | 0.092 | 0.21 | YES
11 | PSMB8 | PSMB8 | PSMB8 | 3462 | 0.088 | 0.23 | YES
12 | PSMC5 | PSMC5 | PSMC5 | 3504 | 0.086 | 0.26 | YES
13 | PSMC3 | PSMC3 | PSMC3 | 3582 | 0.084 | 0.28 | YES
14 | PSMB10 | PSMB10 | PSMB10 | 3616 | 0.083 | 0.31 | YES
15 | PSMD4 | PSMD4 | PSMD4 | 3651 | 0.082 | 0.34 | YES
16 | PSMD13 | PSMD13 | PSMD13 | 3753 | 0.078 | 0.36 | YES
17 | PSME2 | PSME2 | PSME2 | 3912 | 0.074 | 0.37 | YES
18 | PSMF1 | PSMF1 | PSMF1 | 4032 | 0.07 | 0.39 | YES
19 | RBX1 | RBX1 | RBX1 | 4482 | 0.059 | 0.39 | YES
20 | PSMA4 | PSMA4 | PSMA4 | 4525 | 0.057 | 0.4 | YES
21 | PSMB5 | PSMB5 | PSMB5 | 4836 | 0.049 | 0.4 | YES
22 | PSMB4 | PSMB4 | PSMB4 | 5068 | 0.044 | 0.41 | YES
23 | PSMA6 | PSMA6 | PSMA6 | 5242 | 0.04 | 0.41 | YES
24 | PSMC1 | PSMC1 | PSMC1 | 5341 | 0.037 | 0.42 | YES
25 | RPS27A | RPS27A | RPS27A | 5515 | 0.033 | 0.42 | YES
26 | TCEB1 | TCEB1 | TCEB1 | 6163 | 0.019 | 0.39 | NO
27 | PSMD8 | PSMD8 | PSMD8 | 6256 | 0.017 | 0.39 | NO
28 | PSMB7 | PSMB7 | PSMB7 | 6305 | 0.016 | 0.39 | NO
29 | PSME1 | PSME1 | PSME1 | 6498 | 0.011 | 0.39 | NO
30 | PSMA3 | PSMA3 | PSMA3 | 6620 | 0.0083 | 0.38 | NO
31 | PSMA7 | PSMA7 | PSMA7 | 6781 | 0.0049 | 0.38 | NO
32 | PSMD14 | PSMD14 | PSMD14 | 6898 | 0.0023 | 0.37 | NO
33 | PSMD7 | PSMD7 | PSMD7 | 7134 | -0.0025 | 0.36 | NO
34 | PSMA2 | PSMA2 | PSMA2 | 7567 | -0.012 | 0.34 | NO
35 | PSMC6 | PSMC6 | PSMC6 | 7607 | -0.012 | 0.34 | NO
36 | PSMA1 | PSMA1 | PSMA1 | 7708 | -0.015 | 0.34 | NO
37 | PSMB1 | PSMB1 | PSMB1 | 8066 | -0.023 | 0.33 | NO
38 | PSMD1 | PSMD1 | PSMD1 | 8110 | -0.024 | 0.33 | NO
39 | PSMC2 | PSMC2 | PSMC2 | 8243 | -0.027 | 0.34 | NO
40 | PSMD11 | PSMD11 | PSMD11 | 8256 | -0.027 | 0.34 | NO
41 | PSMD12 | PSMD12 | PSMD12 | 8298 | -0.028 | 0.35 | NO
42 | PSMD3 | PSMD3 | PSMD3 | 8649 | -0.036 | 0.35 | NO
43 | CUL5 | CUL5 | CUL5 | 9018 | -0.045 | 0.34 | NO
44 | PSMD10 | PSMD10 | PSMD10 | 10070 | -0.069 | 0.31 | NO
45 | PSMD6 | PSMD6 | PSMD6 | 10163 | -0.072 | 0.33 | NO
46 | PSME4 | PSME4 | PSME4 | 10314 | -0.075 | 0.34 | NO
47 | PSMD2 | PSMD2 | PSMD2 | 10396 | -0.078 | 0.37 | NO
48 | PSMD5 | PSMD5 | PSMD5 | 13390 | -0.18 | 0.26 | NO

Figure S79. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME P53 INDEPENDENT G1 S DNA DAMAGE CHECKPOINT.

Figure S80. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME P53 INDEPENDENT G1 S DNA DAMAGE CHECKPOINT, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

For the top enriched genes, if you want to check whether they are

- up-regulated, please check the list of up-regulated genes

- down-regulated, please check the list of down-regulated genes

Expression level

For the top enriched genes, if you want to check whether they are

- highly expressed genes, please check the list of high (top 30%) expressed genes

- low expressed genes, please check the list of low (bottom 30%) expressed genes

An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap

Significant gene list

For the top enriched genes, if you want to check whether they are

- significantly differently expressed genes by eBayes lm fit, please check the list of significant genes

Subtype clus5 enriched pathways

Table 7. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus5. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
KEGG GLYCOLYSIS GLUCONEOGENESIS | 58 | genes.ES.table | 0.7 | 2.1 | 0 | 0.014 | 0.042 | 0.31 | 0.094 | 0.28 | 0 | 0.002
KEGG CITRATE CYCLE TCA CYCLE | 29 | genes.ES.table | 0.6 | 1.6 | 0.12 | 0.21 | 0.95 | 0.48 | 0.28 | 0.35 | 0.14 | 0.014
KEGG PENTOSE PHOSPHATE PATHWAY | 25 | genes.ES.table | 0.54 | 1.6 | 0.036 | 0.18 | 0.94 | 0.2 | 0.12 | 0.18 | 0.12 | 0.011
KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS | 27 | genes.ES.table | 0.78 | 1.5 | 0.042 | 0.24 | 0.97 | 0.52 | 0.061 | 0.49 | 0.17 | 0.018
KEGG FRUCTOSE AND MANNOSE METABOLISM | 33 | genes.ES.table | 0.68 | 2.1 | 0 | 0.011 | 0.05 | 0.15 | 0.034 | 0.15 | 0 | 0
KEGG FATTY ACID METABOLISM | 39 | genes.ES.table | 0.8 | 1.9 | 0 | 0.033 | 0.24 | 0.62 | 0.14 | 0.53 | 0 | 0.001
KEGG STEROID HORMONE BIOSYNTHESIS | 51 | genes.ES.table | 0.81 | 1.8 | 0 | 0.066 | 0.64 | 0.49 | 0.061 | 0.46 | 0.024 | 0.001
KEGG PURINE METABOLISM | 153 | genes.ES.table | 0.41 | 1.8 | 0.002 | 0.067 | 0.64 | 0.2 | 0.15 | 0.17 | 0.024 | 0.001
KEGG PYRIMIDINE METABOLISM | 97 | genes.ES.table | 0.49 | 2.2 | 0 | 0.011 | 0.03 | 0.093 | 0.068 | 0.087 | 0 | 0.002
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM | 32 | genes.ES.table | 0.78 | 2 | 0 | 0.028 | 0.18 | 0.53 | 0.12 | 0.47 | 0 | 0.003

genes ES table in pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS

Table S41. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | SULT2A1 | SULT2A1 | SULT2A1 | 26 | 2 | 0.087 | YES
2 | APOA5 | APOA5 | APOA5 | 29 | 1.9 | 0.17 | YES
3 | APOA1 | APOA1 | APOA1 | 83 | 1.5 | 0.24 | YES
4 | FABP1 | FABP1 | FABP1 | 121 | 1.3 | 0.3 | YES
5 | ABCB4 | ABCB4 | ABCB4 | 142 | 1.2 | 0.35 | YES
6 | CYP7A1 | CYP7A1 | CYP7A1 | 144 | 1.2 | 0.4 | YES
7 | CYP1A1 | CYP1A1 | CYP1A1 | 154 | 1.1 | 0.46 | YES
8 | APOA2 | APOA2 | APOA2 | 155 | 1.1 | 0.51 | YES
9 | HMGCS2 | HMGCS2 | HMGCS2 | 175 | 1 | 0.55 | YES
10 | CYP4A11 | CYP4A11 | CYP4A11 | 239 | 0.83 | 0.59 | YES
11 | G0S2 | G0S2 | G0S2 | 435 | 0.52 | 0.6 | YES
12 | ACSL1 | ACSL1 | ACSL1 | 473 | 0.49 | 0.62 | YES
13 | UGT1A9 | UGT1A9 | UGT1A9 | 562 | 0.43 | 0.64 | YES
14 | CD36 | CD36 | CD36 | 651 | 0.38 | 0.65 | YES
15 | PLIN2 | PLIN2 | PLIN2 | 655 | 0.38 | 0.66 | YES
16 | ANGPTL4 | ANGPTL4 | ANGPTL4 | 805 | 0.33 | 0.67 | YES
17 | ANKRD1 | ANKRD1 | ANKRD1 | 1135 | 0.26 | 0.66 | YES
18 | AGT | AGT | AGT | 1136 | 0.26 | 0.68 | YES
19 | ALAS1 | ALAS1 | ALAS1 | 1388 | 0.22 | 0.67 | YES
20 | HMGCS1 | HMGCS1 | HMGCS1 | 1538 | 0.2 | 0.67 | YES
21 | ABCA1 | ABCA1 | ABCA1 | 1641 | 0.19 | 0.68 | YES
22 | ACADM | ACADM | ACADM | 1865 | 0.17 | 0.67 | YES
23 | CPT2 | CPT2 | CPT2 | 1964 | 0.16 | 0.67 | YES
24 | PPARA | PPARA | PPARA | 1990 | 0.16 | 0.68 | YES
25 | ACOX1 | ACOX1 | ACOX1 | 2024 | 0.16 | 0.68 | YES
26 | ARNTL | ARNTL | ARNTL | 2245 | 0.15 | 0.68 | NO
27 | GRHL1 | GRHL1 | GRHL1 | 2312 | 0.14 | 0.68 | NO
28 | TRIB3 | TRIB3 | TRIB3 | 2442 | 0.14 | 0.68 | NO
29 | MED8 | MED8 | MED8 | 3004 | 0.11 | 0.65 | NO
30 | HMGCR | HMGCR | HMGCR | 3112 | 0.1 | 0.65 | NO
31 | FADS1 | FADS1 | FADS1 | 3220 | 0.099 | 0.65 | NO
32 | NPAS2 | NPAS2 | NPAS2 | 3223 | 0.099 | 0.66 | NO
33 | MED31 | MED31 | MED31 | 3416 | 0.094 | 0.65 | NO
34 | CCNC | CCNC | CCNC | 3705 | 0.085 | 0.64 | NO
35 | NCOA2 | NCOA2 | NCOA2 | 3791 | 0.083 | 0.64 | NO
36 | SREBF2 | SREBF2 | SREBF2 | 4155 | 0.073 | 0.62 | NO
37 | PPARGC1B | PPARGC1B | PPARGC1B | 4367 | 0.068 | 0.61 | NO
38 | PPARGC1A | PPARGC1A | PPARGC1A | 4518 | 0.064 | 0.61 | NO
39 | EP300 | EP300 | EP300 | 4615 | 0.062 | 0.6 | NO
40 | PEX11A | PEX11A | PEX11A | 4914 | 0.055 | 0.59 | NO
41 | TIAM2 | TIAM2 | TIAM2 | 5094 | 0.052 | 0.58 | NO
42 | CPT1A | CPT1A | CPT1A | 5540 | 0.043 | 0.56 | NO
43 | SREBF1 | SREBF1 | SREBF1 | 5824 | 0.038 | 0.55 | NO
44 | MED23 | MED23 | MED23 | 5963 | 0.036 | 0.54 | NO
45 | CDK8 | CDK8 | CDK8 | 6256 | 0.032 | 0.52 | NO
46 | ESRRA | ESRRA | ESRRA | 6409 | 0.03 | 0.52 | NO
47 | MED29 | MED29 | MED29 | 6459 | 0.029 | 0.52 | NO
48 | MED10 | MED10 | MED10 | 6523 | 0.028 | 0.51 | NO
49 | ME1 | ME1 | ME1 | 6698 | 0.026 | 0.5 | NO
50 | TEAD1 | TEAD1 | TEAD1 | 6893 | 0.024 | 0.5 | NO
51 | CDK19 | CDK19 | CDK19 | 6987 | 0.022 | 0.49 | NO
52 | RXRA | RXRA | RXRA | 7058 | 0.021 | 0.49 | NO
53 | NFYB | NFYB | NFYB | 7150 | 0.02 | 0.48 | NO
54 | NCOA3 | NCOA3 | NCOA3 | 7449 | 0.016 | 0.47 | NO
55 | MED11 | MED11 | MED11 | 7594 | 0.014 | 0.46 | NO
56 | TBL1X | TBL1X | TBL1X | 7812 | 0.012 | 0.45 | NO
57 | PPARG | PPARG | PPARG | 8013 | 0.0092 | 0.44 | NO
58 | HDAC3 | HDAC3 | HDAC3 | 8129 | 0.008 | 0.43 | NO
59 | RORA | RORA | RORA | 8204 | 0.007 | 0.43 | NO
60 | MED9 | MED9 | MED9 | 8990 | -0.0021 | 0.38 | NO
61 | GLIPR1 | GLIPR1 | GLIPR1 | 9568 | -0.0085 | 0.35 | NO
62 | FHL2 | FHL2 | FHL2 | 9647 | -0.0095 | 0.35 | NO
63 | MED1 | MED1 | MED1 | 9875 | -0.012 | 0.34 | NO
64 | MED25 | MED25 | MED25 | 9885 | -0.012 | 0.34 | NO
65 | MED6 | MED6 | MED6 | 9947 | -0.013 | 0.34 | NO
66 | YAP1 | YAP1 | YAP1 | 10003 | -0.013 | 0.33 | NO
67 | MED13L | MED13L | MED13L | 10117 | -0.015 | 0.33 | NO
68 | MED26 | MED26 | MED26 | 10151 | -0.015 | 0.33 | NO
69 | NCOR1 | NCOR1 | NCOR1 | 10218 | -0.016 | 0.32 | NO
70 | MED14 | MED14 | MED14 | 10229 | -0.016 | 0.32 | NO
71 | MED4 | MED4 | MED4 | 10281 | -0.017 | 0.32 | NO
72 | MED18 | MED18 | MED18 | 10438 | -0.019 | 0.31 | NO
73 | NCOA6 | NCOA6 | NCOA6 | 10527 | -0.02 | 0.31 | NO
74 | MED15 | MED15 | MED15 | 10546 | -0.02 | 0.31 | NO
75 | CLOCK | CLOCK | CLOCK | 10649 | -0.021 | 0.3 | NO
76 | NFYA | NFYA | NFYA | 11046 | -0.026 | 0.28 | NO
77 | TXNRD1 | TXNRD1 | TXNRD1 | 11066 | -0.026 | 0.28 | NO
78 | MED7 | MED7 | MED7 | 11226 | -0.029 | 0.28 | NO
79 | MED12 | MED12 | MED12 | 11230 | -0.029 | 0.28 | NO
80 | CREBBP | CREBBP | CREBBP | 11359 | -0.03 | 0.27 | NO
81 | MED16 | MED16 | MED16 | 12225 | -0.042 | 0.22 | NO
82 | SLC27A1 | SLC27A1 | SLC27A1 | 12327 | -0.044 | 0.22 | NO
83 | TBL1XR1 | TBL1XR1 | TBL1XR1 | 12414 | -0.045 | 0.22 | NO
84 | MED24 | MED24 | MED24 | 12650 | -0.049 | 0.21 | NO
85 | PRIC285 | PRIC285 | PRIC285 | 12882 | -0.053 | 0.2 | NO
86 | MED19 | MED19 | MED19 | 12960 | -0.054 | 0.2 | NO
87 | CTGF | CTGF | CTGF | 12990 | -0.054 | 0.2 | NO
88 | NCOA1 | NCOA1 | NCOA1 | 13130 | -0.056 | 0.19 | NO
89 | NRF1 | NRF1 | NRF1 | 13517 | -0.063 | 0.17 | NO
90 | WWTR1 | WWTR1 | WWTR1 | 13856 | -0.07 | 0.16 | NO
91 | TEAD2 | TEAD2 | TEAD2 | 13980 | -0.072 | 0.15 | NO
92 | TGS1 | TGS1 | TGS1 | 14177 | -0.076 | 0.15 | NO
93 | TEAD3 | TEAD3 | TEAD3 | 14408 | -0.082 | 0.14 | NO
94 | TEAD4 | TEAD4 | TEAD4 | 14578 | -0.086 | 0.13 | NO
95 | FDFT1 | FDFT1 | FDFT1 | 14693 | -0.089 | 0.13 | NO
96 | MED21 | MED21 | MED21 | 15304 | -0.11 | 0.1 | NO
97 | MED27 | MED27 | MED27 | 15307 | -0.11 | 0.1 | NO
98 | MED30 | MED30 | MED30 | 15546 | -0.12 | 0.097 | NO
99 | MED17 | MED17 | MED17 | 15610 | -0.12 | 0.099 | NO
100 | MED22 | MED22 | MED22 | 15655 | -0.12 | 0.1 | NO
101 | TNFRSF21 | TNFRSF21 | TNFRSF21 | 15828 | -0.13 | 0.098 | NO
102 | MED20 | MED20 | MED20 | 16432 | -0.16 | 0.072 | NO
103 | NR1D1 | NR1D1 | NR1D1 | 17067 | -0.22 | 0.047 | NO
104 | SMARCD3 | SMARCD3 | SMARCD3 | 17338 | -0.24 | 0.043 | NO

Figure S81. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS.

Figure S82. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

Table S42. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | AKR1D1 | AKR1D1 | AKR1D1 | 14 | 2.1 | 0.023 | YES
2 | SLC10A1 | SLC10A1 | SLC10A1 | 20 | 2 | 0.046 | YES
3 | SULT2A1 | SULT2A1 | SULT2A1 | 26 | 2 | 0.068 | YES
4 | CYP8B1 | CYP8B1 | CYP8B1 | 28 | 1.9 | 0.09 | YES
5 | APOA5 | APOA5 | APOA5 | 29 | 1.9 | 0.11 | YES
6 | MTTP | MTTP | MTTP | 47 | 1.8 | 0.13 | YES
7 | ABCB11 | ABCB11 | ABCB11 | 48 | 1.8 | 0.15 | YES
8 | SRD5A2 | SRD5A2 | SRD5A2 | 57 | 1.7 | 0.17 | YES
9 | APOC3 | APOC3 | APOC3 | 61 | 1.7 | 0.19 | YES
10 | APOA1 | APOA1 | APOA1 | 83 | 1.5 | 0.2 | YES
11 | LPA | LPA | LPA | 100 | 1.4 | 0.22 | YES
12 | FABP1 | FABP1 | FABP1 | 121 | 1.3 | 0.23 | YES
13 | APOC2 | APOC2 | APOC2 | 123 | 1.3 | 0.25 | YES
14 | ENPP7 | ENPP7 | ENPP7 | 126 | 1.3 | 0.26 | YES
15 | ABCG8 | ABCG8 | ABCG8 | 134 | 1.2 | 0.28 | YES
16 | PLA2G2A | PLA2G2A | PLA2G2A | 135 | 1.2 | 0.29 | YES
17 | ABCB4 | ABCB4 | ABCB4 | 142 | 1.2 | 0.3 | YES
18 | CYP7A1 | CYP7A1 | CYP7A1 | 144 | 1.2 | 0.32 | YES
19 | ABCG5 | ABCG5 | ABCG5 | 146 | 1.2 | 0.33 | YES
20 | CYP1A1 | CYP1A1 | CYP1A1 | 154 | 1.1 | 0.34 | YES
21 | APOA2 | APOA2 | APOA2 | 155 | 1.1 | 0.36 | YES
22 | SLC27A5 | SLC27A5 | SLC27A5 | 156 | 1.1 | 0.37 | YES
23 | SLCO1B1 | SLCO1B1 | SLCO1B1 | 174 | 1 | 0.38 | YES
24 | HMGCS2 | HMGCS2 | HMGCS2 | 175 | 1 | 0.39 | YES
25 | AKR1C4 | AKR1C4 | AKR1C4 | 178 | 1 | 0.4 | YES
26 | CYP39A1 | CYP39A1 | CYP39A1 | 188 | 1 | 0.42 | YES
27 | GBA3 | GBA3 | GBA3 | 215 | 0.92 | 0.42 | YES
28 | ACOX2 | ACOX2 | ACOX2 | 226 | 0.87 | 0.43 | YES
29 | CYP4A11 | CYP4A11 | CYP4A11 | 239 | 0.83 | 0.44 | YES
30 | NEU4 | NEU4 | NEU4 | 241 | 0.83 | 0.45 | YES
31 | PLIN1 | PLIN1 | PLIN1 | 242 | 0.83 | 0.46 | YES
32 | GPD1 | GPD1 | GPD1 | 273 | 0.77 | 0.47 | YES
33 | PIK3C2G | PIK3C2G | PIK3C2G | 283 | 0.74 | 0.48 | YES
34 | ACADL | ACADL | ACADL | 288 | 0.72 | 0.48 | YES
35 | BDH1 | BDH1 | BDH1 | 330 | 0.66 | 0.49 | YES
36 | SLCO1B3 | SLCO1B3 | SLCO1B3 | 335 | 0.64 | 0.5 | YES
37 | GPAM | GPAM | GPAM | 356 | 0.61 | 0.5 | YES
38 | CYP17A1 | CYP17A1 | CYP17A1 | 360 | 0.61 | 0.51 | YES
39 | DGAT2 | DGAT2 | DGAT2 | 386 | 0.57 | 0.52 | YES
40 | ALB | ALB | ALB | 388 | 0.57 | 0.52 | YES
41 | APOB | APOB | APOB | 410 | 0.54 | 0.53 | YES
42 | G0S2 | G0S2 | G0S2 | 435 | 0.52 | 0.53 | YES
43 | PLA2G5 | PLA2G5 | PLA2G5 | 454 | 0.5 | 0.54 | YES
44 | ACSL1 | ACSL1 | ACSL1 | 473 | 0.49 | 0.54 | YES
45 | HSD11B1 | HSD11B1 | HSD11B1 | 485 | 0.48 | 0.55 | YES
46 | APOE | APOE | APOE | 501 | 0.47 | 0.55 | YES
47 | ELOVL2 | ELOVL2 | ELOVL2 | 502 | 0.47 | 0.56 | YES
48 | SLC27A2 | SLC27A2 | SLC27A2 | 507 | 0.46 | 0.56 | YES
49 | CYP11A1 | CYP11A1 | CYP11A1 | 536 | 0.45 | 0.56 | YES
50 | UGT1A9 | UGT1A9 | UGT1A9 | 562 | 0.43 | 0.57 | YES
51 | BAAT | BAAT | BAAT | 568 | 0.42 | 0.57 | YES
52 | CYP27A1 | CYP27A1 | CYP27A1 | 581 | 0.42 | 0.58 | YES
53 | SLCO1A2 | SLCO1A2 | SLCO1A2 | 635 | 0.39 | 0.58 | YES
54 | CD36 | CD36 | CD36 | 651 | 0.38 | 0.58 | YES
55 | PLIN2 | PLIN2 | PLIN2 | 655 | 0.38 | 0.58 | YES
56 | LCAT | LCAT | LCAT | 681 | 0.37 | 0.59 | YES
57 | ANGPTL4 | ANGPTL4 | ANGPTL4 | 805 | 0.33 | 0.58 | YES
58 | CETP | CETP | CETP | 833 | 0.32 | 0.59 | YES
59 | ACSL6 | ACSL6 | ACSL6 | 864 | 0.31 | 0.59 | YES
60 | GC | GC | GC | 867 | 0.31 | 0.59 | YES
61 | ARSF | ARSF | ARSF | 940 | 0.29 | 0.59 | YES
62 | ELOVL6 | ELOVL6 | ELOVL6 | 972 | 0.28 | 0.59 | YES
63 | CHPT1 | CHPT1 | CHPT1 | 1003 | 0.28 | 0.59 | YES
64 | LIPC | LIPC | LIPC | 1012 | 0.28 | 0.6 | YES
65 | SLC25A20 | SLC25A20 | SLC25A20 | 1026 | 0.27 | 0.6 | YES
66 | ANKRD1 | ANKRD1 | ANKRD1 | 1135 | 0.26 | 0.6 | YES
67 | AGT | AGT | AGT | 1136 | 0.26 | 0.6 | YES
68 | MCEE | MCEE | MCEE | 1162 | 0.25 | 0.6 | YES
69 | ACAT1 | ACAT1 | ACAT1 | 1163 | 0.25 | 0.6 | YES
70 | BCMO1 | BCMO1 | BCMO1 | 1193 | 0.25 | 0.6 | YES
71 | A2M | A2M | A2M | 1205 | 0.24 | 0.61 | YES
72 | ETNK2 | ETNK2 | ETNK2 | 1230 | 0.24 | 0.61 | YES
73 | PHYH | PHYH | PHYH | 1233 | 0.24 | 0.61 | YES
74 | ACSL5 | ACSL5 | ACSL5 | 1246 | 0.24 | 0.61 | YES
75 | SCARB1 | SCARB1 | SCARB1 | 1368 | 0.22 | 0.61 | YES
76 | ELOVL7 | ELOVL7 | ELOVL7 | 1369 | 0.22 | 0.61 | YES
77 | ALAS1 | ALAS1 | ALAS1 | 1388 | 0.22 | 0.61 | YES
78 | STARD5 | STARD5 | STARD5 | 1410 | 0.22 | 0.61 | YES
79 | FABP4 | FABP4 | FABP4 | 1465 | 0.21 | 0.61 | YES
80 | ARSJ | ARSJ | ARSJ | 1517 | 0.2 | 0.61 | YES
81 | HMGCS1 | HMGCS1 | HMGCS1 | 1538 | 0.2 | 0.61 | YES
82 | SC5DL | SC5DL | SC5DL | 1603 | 0.19 | 0.61 | YES
83 | FASN | FASN | FASN | 1623 | 0.19 | 0.61 | YES
84 | ABCA1 | ABCA1 | ABCA1 | 1641 | 0.19 | 0.61 | YES
85 | TM7SF2 | TM7SF2 | TM7SF2 | 1671 | 0.19 | 0.62 | YES
86 | ACAA1 | ACAA1 | ACAA1 | 1754 | 0.18 | 0.61 | YES
87 | HMGCL | HMGCL | HMGCL | 1756 | 0.18 | 0.61 | YES
88 | PEMT | PEMT | PEMT | 1764 | 0.18 | 0.62 | YES
89 | DHCR24 | DHCR24 | DHCR24 | 1774 | 0.18 | 0.62 | YES
90 | ACACB | ACACB | ACACB | 1791 | 0.18 | 0.62 | YES
91 | SCP2 | SCP2 | SCP2 | 1818 | 0.18 | 0.62 | YES
92 | STARD4 | STARD4 | STARD4 | 1858 | 0.17 | 0.62 | YES
93 | ACADM | ACADM | ACADM | 1865 | 0.17 | 0.62 | YES
94 | ARSE | ARSE | ARSE | 1902 | 0.17 | 0.62 | YES
95 | PIK3R1 | PIK3R1 | PIK3R1 | 1936 | 0.17 | 0.62 | YES
96 | CPT2 | CPT2 | CPT2 | 1964 | 0.16 | 0.62 | YES
97 | PPARA | PPARA | PPARA | 1990 | 0.16 | 0.62 | YES
98 | HSD17B3 | HSD17B3 | HSD17B3 | 2004 | 0.16 | 0.62 | YES
99 | ACOX1 | ACOX1 | ACOX1 | 2024 | 0.16 | 0.62 | YES
100 | PLD1 | PLD1 | PLD1 | 2026 | 0.16 | 0.62 | YES
101 | SAR1B | SAR1B | SAR1B | 2045 | 0.16 | 0.62 | YES
102 | PRKAA2 | PRKAA2 | PRKAA2 | 2091 | 0.16 | 0.62 | NO
103 | ECHS1 | ECHS1 | ECHS1 | 2114 | 0.15 | 0.62 | NO
104 | ELOVL3 | ELOVL3 | ELOVL3 | 2155 | 0.15 | 0.62 | NO
105 | ARNTL | ARNTL | ARNTL | 2245 | 0.15 | 0.62 | NO
106 | PPAP2B | PPAP2B | PPAP2B | 2254 | 0.14 | 0.62 | NO
107 | SDC1 | SDC1 | SDC1 | 2294 | 0.14 | 0.62 | NO
108 | P4HB | P4HB | P4HB | 2306 | 0.14 | 0.62 | NO
109 | GRHL1 | GRHL1 | GRHL1 | 2312 | 0.14 | 0.62 | NO
110 | PHOSPHO1 | PHOSPHO1 | PHOSPHO1 | 2365 | 0.14 | 0.62 | NO
111 | ASAH2 | ASAH2 | ASAH2 | 2389 | 0.14 | 0.62 | NO
112 | TRIB3 | TRIB3 | TRIB3 | 2442 | 0.14 | 0.62 | NO
113 | MUT | MUT | MUT | 2466 | 0.13 | 0.62 | NO
114 | HSD17B4 | HSD17B4 | HSD17B4 | 2509 | 0.13 | 0.62 | NO
115 | ACADS | ACADS | ACADS | 2519 | 0.13 | 0.62 | NO
116 | SRD5A1 | SRD5A1 | SRD5A1 | 2538 | 0.13 | 0.62 | NO
117 | AMACR | AMACR | AMACR | 2687 | 0.12 | 0.62 | NO
118 | GAL3ST1 | GAL3ST1 | GAL3ST1 | 2752 | 0.12 | 0.61 | NO
119 | PIK3R5 | PIK3R5 | PIK3R5 | 2819 | 0.12 | 0.61 | NO
120 | ELOVL5 | ELOVL5 | ELOVL5 | 2884 | 0.11 | 0.61 | NO
121 | EBP | EBP | EBP | 2958 | 0.11 | 0.61 | NO
122 | COL4A3BP | COL4A3BP | COL4A3BP | 2984 | 0.11 | 0.6 | NO
123 | PLA2G2D | PLA2G2D | PLA2G2D | 2997 | 0.11 | 0.61 | NO
124 | MED8 | MED8 | MED8 | 3004 | 0.11 | 0.61 | NO
125 | HMGCR | HMGCR | HMGCR | 3112 | 0.1 | 0.6 | NO
126 | IDI1 | IDI1 | IDI1 | 3124 | 0.1 | 0.6 | NO
127 | HEXB | HEXB | HEXB | 3184 | 0.1 | 0.6 | NO
128 | HSD17B1 | HSD17B1 | HSD17B1 | 3185 | 0.1 | 0.6 | NO
129 | SYNJ1 | SYNJ1 | SYNJ1 | 3186 | 0.1 | 0.6 | NO
130 | DHCR7 | DHCR7 | DHCR7 | 3197 | 0.1 | 0.6 | NO
131 | FADS1 | FADS1 | FADS1 | 3220 | 0.099 | 0.6 | NO
132 | NPAS2 | NPAS2 | NPAS2 | 3223 | 0.099 | 0.6 | NO
133 | IDH1 | IDH1 | IDH1 | 3226 | 0.099 | 0.6 | NO
134 | PRKACB | PRKACB | PRKACB | 3272 | 0.097 | 0.6 | NO
135 | ARSK | ARSK | ARSK | 3278 | 0.097 | 0.6 | NO
136 | CYP27B1 | CYP27B1 | CYP27B1 | 3328 | 0.096 | 0.6 | NO
137 | MED31 | MED31 | MED31 | 3416 | 0.094 | 0.6 | NO
138 | ACADVL | ACADVL | ACADVL | 3459 | 0.092 | 0.6 | NO
139 | MTMR4 | MTMR4 | MTMR4 | 3469 | 0.092 | 0.6 | NO
140 | PI4K2B | PI4K2B | PI4K2B | 3480 | 0.092 | 0.6 | NO
141 | LBR | LBR | LBR | 3501 | 0.091 | 0.6 | NO
142 | ARSB | ARSB | ARSB | 3555 | 0.09 | 0.6 | NO
143 | CROT | CROT | CROT | 3645 | 0.087 | 0.59 | NO
144 | PPAP2A | PPAP2A | PPAP2A | 3676 | 0.086 | 0.59 | NO
145 | CRLS1 | CRLS1 | CRLS1 | 3683 | 0.086 | 0.59 | NO
146 | CCNC | CCNC | CCNC | 3705 | 0.085 | 0.59 | NO
147 | ELOVL1 | ELOVL1 | ELOVL1 | 3744 | 0.084 | 0.59 | NO
148 | NCOA2 | NCOA2 | NCOA2 | 3791 | 0.083 | 0.59 | NO
149 | PCYT2 | PCYT2 | PCYT2 | 3898 | 0.079 | 0.58 | NO
150 | PCYT1A | PCYT1A | PCYT1A | 3958 | 0.078 | 0.58 | NO
151 | ACSL3 | ACSL3 | ACSL3 | 4014 | 0.076 | 0.58 | NO
152 | HADHB | HADHB | HADHB | 4022 | 0.076 | 0.58 | NO
153 | FAR2 | FAR2 | FAR2 | 4025 | 0.076 | 0.58 | NO
154 | SLC25A17 | SLC25A17 | SLC25A17 | 4076 | 0.075 | 0.58 | NO
155 | EPT1 | EPT1 | EPT1 | 4092 | 0.074 | 0.58 | NO
156 | SYNJ2 | SYNJ2 | SYNJ2 | 4142 | 0.073 | 0.58 | NO
157 | SREBF2 | SREBF2 | SREBF2 | 4155 | 0.073 | 0.58 | NO
158 | CYP2R1 | CYP2R1 | CYP2R1 | 4173 | 0.072 | 0.58 | NO
159 | OSBP | OSBP | OSBP | 4176 | 0.072 | 0.58 | NO
160 | ARSG | ARSG | ARSG | 4262 | 0.07 | 0.57 | NO
161 | SMPD1 | SMPD1 | SMPD1 | 4297 | 0.069 | 0.57 | NO
162 | GALC | GALC | GALC | 4313 | 0.069 | 0.57 | NO
163 | CRAT | CRAT | CRAT | 4335 | 0.068 | 0.57 | NO
164 | PPARGC1B | PPARGC1B | PPARGC1B | 4367 | 0.068 | 0.57 | NO
165 | MVK | MVK | MVK | 4379 | 0.067 | 0.57 | NO
166 | PI4K2A | PI4K2A | PI4K2A | 4405 | 0.067 | 0.57 | NO
167 | AGPAT3 | AGPAT3 | AGPAT3 | 4456 | 0.065 | 0.57 | NO
168 | LSS | LSS | LSS | 4469 | 0.065 | 0.57 | NO
169 | PPARGC1A | PPARGC1A | PPARGC1A | 4518 | 0.064 | 0.57 | NO
170 | AGPS | AGPS | AGPS | 4524 | 0.064 | 0.57 | NO
171 | MBOAT7 | MBOAT7 | MBOAT7 | 4529 | 0.064 | 0.57 | NO
172 | LPIN2 | LPIN2 | LPIN2 | 4590 | 0.062 | 0.56 | NO
173 | EP300 | EP300 | EP300 | 4615 | 0.062 | 0.56 | NO
174 | LDLR | LDLR | LDLR | 4649 | 0.061 | 0.56 | NO
175 | PPM1L | PPM1L | PPM1L | 4653 | 0.061 | 0.56 | NO
176 | LPCAT3 | LPCAT3 | LPCAT3 | 4672 | 0.06 | 0.56 | NO
177 | CYP51A1 | CYP51A1 | CYP51A1 | 4674 | 0.06 | 0.56 | NO
178 | UGCG | UGCG | UGCG | 4790 | 0.058 | 0.56 | NO
179 | SPTLC2 | SPTLC2 | SPTLC2 | 4893 | 0.056 | 0.55 | NO
180 | HADH | HADH | HADH | 4896 | 0.056 | 0.55 | NO
181 | PEX11A | PEX11A | PEX11A | 4914 | 0.055 | 0.55 | NO
182 | PLD3 | PLD3 | PLD3 | 4944 | 0.055 | 0.55 | NO
183 | PRKAG2 | PRKAG2 | PRKAG2 | 5014 | 0.053 | 0.55 | NO
184 | SPHK2 | SPHK2 | SPHK2 | 5020 | 0.053 | 0.55 | NO
185 | PIK3C2B | PIK3C2B | PIK3C2B | 5083 | 0.052 | 0.55 | NO
186 | TIAM2 | TIAM2 | TIAM2 | 5094 | 0.052 | 0.55 | NO
187 | ARSI | ARSI | ARSI | 5102 | 0.052 | 0.55 | NO
188 | GK | GK | GK | 5111 | 0.052 | 0.55 | NO
189 | HSD17B12 | HSD17B12 | HSD17B12 | 5120 | 0.051 | 0.55 | NO
190 | HADHA | HADHA | HADHA | 5144 | 0.051 | 0.55 | NO
191 | PITPNB | PITPNB | PITPNB | 5160 | 0.05 | 0.55 | NO
192 | GPD1L | GPD1L | GPD1L | 5179 | 0.05 | 0.55 | NO
193 | SGPP1 | SGPP1 | SGPP1 | 5237 | 0.049 | 0.54 | NO
194 | HSPG2 | HSPG2 | HSPG2 | 5272 | 0.048 | 0.54 | NO
195 | PCCB | PCCB | PCCB | 5362 | 0.047 | 0.54 | NO
196 | LPGAT1 | LPGAT1 | LPGAT1 | 5396 | 0.046 | 0.54 | NO
197 | PIK3R3 | PIK3R3 | PIK3R3 | 5445 | 0.045 | 0.53 | NO
198 | PRKACA | PRKACA | PRKACA | 5473 | 0.044 | 0.53 | NO
199 | HSD3B7 | HSD3B7 | HSD3B7 | 5482 | 0.044 | 0.53 | NO
200 | CPT1A | CPT1A | CPT1A | 5540 | 0.043 | 0.53 | NO
201 | AGPAT9 | AGPAT9 | AGPAT9 | 5549 | 0.043 | 0.53 | NO
202 | SGMS2 | SGMS2 | SGMS2 | 5559 | 0.043 | 0.53 | NO
203 | PI4KA | PI4KA | PI4KA | 5601 | 0.042 | 0.53 | NO
204 | PRKAB2 | PRKAB2 | PRKAB2 | 5699 | 0.04 | 0.52 | NO
205 | CEPT1 | CEPT1 | CEPT1 | 5743 | 0.04 | 0.52 | NO
206 | ARSA | ARSA | ARSA | 5814 | 0.038 | 0.52 | NO
207 | PSAP | PSAP | PSAP | 5822 | 0.038 | 0.52 | NO
208 | SREBF1 | SREBF1 | SREBF1 | 5824 | 0.038 | 0.52 | NO
209 | RDH11 | RDH11 | RDH11 | 5839 | 0.038 | 0.52 | NO
210 | GM2A | GM2A | GM2A | 5894 | 0.037 | 0.51 | NO
211 | GLA | GLA | GLA | 5908 | 0.037 | 0.51 | NO
212 | MED23 | MED23 | MED23 | 5963 | 0.036 | 0.51 | NO
213 | ACER3 | ACER3 | ACER3 | 5964 | 0.036 | 0.51 | NO
214 | PNPLA8 | PNPLA8 | PNPLA8 | 6009 | 0.036 | 0.51 | NO
215 | LCLAT1 | LCLAT1 | LCLAT1 | 6052 | 0.035 | 0.51 | NO
216 | HACL1 | HACL1 | HACL1 | 6076 | 0.035 | 0.51 | NO
217 | SQLE | SQLE | SQLE | 6096 | 0.034 | 0.51 | NO
218 | PIK3CB | PIK3CB | PIK3CB | 6219 | 0.033 | 0.5 | NO
219 | PIK3CA | PIK3CA | PIK3CA | 6229 | 0.033 | 0.5 | NO
220 | CDK8 | CDK8 | CDK8 | 6256 | 0.032 | 0.5 | NO
221 | SLC44A2 | SLC44A2 | SLC44A2 | 6320 | 0.031 | 0.5 | NO
222 | PRKD1 | PRKD1 | PRKD1 | 6391 | 0.03 | 0.49 | NO
223 | ESRRA | ESRRA | ESRRA | 6409 | 0.03 | 0.49 | NO
224 | MED29 | MED29 | MED29 | 6459 | 0.029 | 0.49 | NO
225 | PIK3R2 | PIK3R2 | PIK3R2 | 6497 | 0.029 | 0.49 | NO
226 | MED10 | MED10 | MED10 | 6523 | 0.028 | 0.49 | NO
227 | SUMF2 | SUMF2 | SUMF2 | 6630 | 0.027 | 0.48 | NO
228 | PLA2G16 | PLA2G16 | PLA2G16 | 6632 | 0.027 | 0.48 | NO
229 | ME1 | ME1 | ME1 | 6698 | 0.026 | 0.48 | NO
230 | MGLL | MGLL | MGLL | 6699 | 0.026 | 0.48 | NO
231 | PCCA | PCCA | PCCA | 6736 | 0.026 | 0.48 | NO
232 | TEAD1 | TEAD1 | TEAD1 | 6893 | 0.024 | 0.47 | NO
233 | LPCAT1 | LPCAT1 | LPCAT1 | 6930 | 0.023 | 0.46 | NO
234 | OCRL | OCRL | OCRL | 6936 | 0.023 | 0.46 | NO
235 | MTM1 | MTM1 | MTM1 | 6942 | 0.023 | 0.46 | NO
236 | CDK19 | CDK19 | CDK19 | 6987 | 0.022 | 0.46 | NO
237 | PIK3C2A | PIK3C2A | PIK3C2A | 7002 | 0.022 | 0.46 | NO
238 | MTMR7 | MTMR7 | MTMR7 | 7005 | 0.022 | 0.46 | NO
239 | AKR1B1 | AKR1B1 | AKR1B1 | 7026 | 0.022 | 0.46 | NO
240 | GLB1 | GLB1 | GLB1 | 7049 | 0.022 | 0.46 | NO
241 | RXRA | RXRA | RXRA | 7058 | 0.021 | 0.46 | NO
242 | ARF1 | ARF1 | ARF1 | 7072 | 0.021 | 0.46 | NO
243 | CH25H | CH25H | CH25H | 7086 | 0.021 | 0.46 | NO
244 | NEU1 | NEU1 | NEU1 | 7130 | 0.02 | 0.46 | NO
245 | NFYB | NFYB | NFYB | 7150 | 0.02 | 0.46 | NO
246 | ACLY | ACLY | ACLY | 7156 | 0.02 | 0.46 | NO
247 | ACACA | ACACA | ACACA | 7181 | 0.02 | 0.46 | NO
248 | SLC44A3 | SLC44A3 | SLC44A3 | 7214 | 0.019 | 0.45 | NO
249 | PPP1CA | PPP1CA | PPP1CA | 7221 | 0.019 | 0.45 | NO
250 | PIK3CG | PIK3CG | PIK3CG | 7376 | 0.017 | 0.44 | NO
251 | LPIN1 | LPIN1 | LPIN1 | 7412 | 0.017 | 0.44 | NO
252 | IDI2 | IDI2 | IDI2 | 7425 | 0.016 | 0.44 | NO
253 | ABCC3 | ABCC3 | ABCC3 | 7426 | 0.016 | 0.44 | NO
254 | SGMS1 | SGMS1 | SGMS1 | 7440 | 0.016 | 0.44 | NO
255 | NCOA3 | NCOA3 | NCOA3 | 7449 | 0.016 | 0.44 | NO
256 | VAPB | VAPB | VAPB | 7562 | 0.014 | 0.44 | NO
257 | MED11 | MED11 | MED11 | 7594 | 0.014 | 0.43 | NO
258 | SLC25A1 | SLC25A1 | SLC25A1 | 7615 | 0.014 | 0.43 | NO
259 | VAC14 | VAC14 | VAC14 | 7649 | 0.013 | 0.43 | NO
260 | ACER2 | ACER2 | ACER2 | 7718 | 0.012 | 0.43 | NO
261 | GBA | GBA | GBA | 7721 | 0.012 | 0.43 | NO
262 | NSDHL | NSDHL | NSDHL | 7741 | 0.012 | 0.43 | NO
263 | PLTP | PLTP | PLTP | 7779 | 0.012 | 0.42 | NO
264 | TBL1X | TBL1X | TBL1X | 7812 | 0.012 | 0.42 | NO
265 | ACOX3 | ACOX3 | ACOX3 | 7887 | 0.011 | 0.42 | NO
266 | ETNK1 | ETNK1 | ETNK1 | 7943 | 0.01 | 0.42 | NO
267 | PPARG | PPARG | PPARG | 8013 | 0.0092 | 0.41 | NO
268 | PLA2G4C | PLA2G4C | PLA2G4C | 8042 | 0.0089 | 0.41 | NO
269 | HEXA | HEXA | HEXA | 8064 | 0.0087 | 0.41 | NO
270 | CPT1B | CPT1B | CPT1B | 8122 | 0.0081 | 0.41 | NO
271 | HDAC3 | HDAC3 | HDAC3 | 8129 | 0.008 | 0.41 | NO
272 | CYP46A1 | CYP46A1 | CYP46A1 | 8142 | 0.0079 | 0.41 | NO
273 | LGMN | LGMN | LGMN | 8182 | 0.0073 | 0.4 | NO
274 | MTMR6 | MTMR6 | MTMR6 | 8202 | 0.007 | 0.4 | NO
275 | RORA | RORA | RORA | 8204 | 0.007 | 0.4 | NO
276 | PPP1CC | PPP1CC | PPP1CC | 8253 | 0.0064 | 0.4 | NO
277 | PIKFYVE | PIKFYVE | PIKFYVE | 8281 | 0.0061 | 0.4 | NO
278 | GNPAT | GNPAT | GNPAT | 8305 | 0.0058 | 0.4 | NO
279 | CDS1 | CDS1 | CDS1 | 8313 | 0.0056 | 0.4 | NO
280 | SACM1L | SACM1L | SACM1L | 8343 | 0.0052 | 0.4 | NO
281 | HSD17B7 | HSD17B7 | HSD17B7 | 8366 | 0.005 | 0.39 | NO
282 | CTSA | CTSA | CTSA | 8440 | 0.0041 | 0.39 | NO
283 | FAR1 | FAR1 | FAR1 | 8459 | 0.0039 | 0.39 | NO
284 | CYP7B1 | CYP7B1 | CYP7B1 | 8523 | 0.0032 | 0.39 | NO
285 | ABHD5 | ABHD5 | ABHD5 | 8569 | 0.0026 | 0.38 | NO
286 | AGPAT5 | AGPAT5 | AGPAT5 | 8739 | 0.00072 | 0.37 | NO
287 | PMVK | PMVK | PMVK | 8755 | 0.00058 | 0.37 | NO
288 | NCOR2 | NCOR2 | NCOR2 | 8825 | -0.00015 | 0.37 | NO
289 | SGPL1 | SGPL1 | SGPL1 | 8917 | -0.0012 | 0.36 | NO
290 | MED9 | MED9 | MED9 | 8990 | -0.0021 | 0.36 | NO
291 | KDSR | KDSR | KDSR | 9005 | -0.0022 | 0.36 | NO
292 | PTEN | PTEN | PTEN | 9083 | -0.003 | 0.36 | NO
293 | CGA | CGA | CGA | 9155 | -0.0039 | 0.35 | NO
294 | DEGS1 | DEGS1 | DEGS1 | 9169 | -0.0041 | 0.35 | NO
295 | FDPS | FDPS | FDPS | 9234 | -0.0049 | 0.35 | NO
296 | MVD | MVD | MVD | 9285 | -0.0053 | 0.34 | NO
297 | CDS2 | CDS2 | CDS2 | 9343 | -0.006 | 0.34 | NO
298 | CERK | CERK | CERK | 9352 | -0.0061 | 0.34 | NO
299 | SUMF1 | SUMF1 | SUMF1 | 9386 | -0.0064 | 0.34 | NO
300 | GLIPR1 | GLIPR1 | GLIPR1 | 9568 | -0.0085 | 0.33 | NO
301 | MTMR1 | MTMR1 | MTMR1 | 9600 | -0.009 | 0.33 | NO
302 | ARF3 | ARF3 | ARF3 | 9639 | -0.0095 | 0.32 | NO
303 | FHL2 | FHL2 | FHL2 | 9647 | -0.0095 | 0.32 | NO
304 | MED1 | MED1 | MED1 | 9875 | -0.012 | 0.31 | NO
305 | MED25 | MED25 | MED25 | 9885 | -0.012 | 0.31 | NO
306 | GGPS1 | GGPS1 | GGPS1 | 9902 | -0.012 | 0.31 | NO
307 | MED6 | MED6 | MED6 | 9947 | -0.013 | 0.31 | NO
308 | PIK3C3 | PIK3C3 | PIK3C3 | 9997 | -0.013 | 0.3 | NO
309 | YAP1 | YAP1 | YAP1 | 10003 | -0.013 | 0.3 | NO
310 | PNPLA3 | PNPLA3 | PNPLA3 | 10019 | -0.014 | 0.3 | NO
311 | SMPD4 | SMPD4 | SMPD4 | 10046 | -0.014 | 0.3 | NO
312 | AGPAT2 | AGPAT2 | AGPAT2 | 10079 | -0.014 | 0.3 | NO
313 | MED13L | MED13L | MED13L | 10117 | -0.015 | 0.3 | NO
314 | MED26 | MED26 | MED26 | 10151 | -0.015 | 0.3 | NO
315 | NCOR1 | NCOR1 | NCOR1 | 10218 | -0.016 | 0.29 | NO
316 | MED14 | MED14 | MED14 | 10229 | -0.016 | 0.29 | NO
317 | MED4 | MED4 | MED4 | 10281 | -0.017 | 0.29 | NO
318 | MTMR3 | MTMR3 | MTMR3 | 10350 | -0.018 | 0.29 | NO
319 | CYP21A2 | CYP21A2 | CYP21A2 | 10362 | -0.018 | 0.29 | NO
320 | MED18 | MED18 | MED18 | 10438 | -0.019 | 0.28 | NO
321 | NCOA6 | NCOA6 | NCOA6 | 10527 | -0.02 | 0.28 | NO
322 | DECR1 | DECR1 | DECR1 | 10540 | -0.02 | 0.28 | NO
323 | MED15 | MED15 | MED15 | 10546 | -0.02 | 0.28 | NO
324 | PLA2G12A | PLA2G12A | PLA2G12A | 10633 | -0.021 | 0.27 | NO
325 | CLOCK | CLOCK | CLOCK | 10649 | -0.021 | 0.27 | NO
326 | MBOAT2 | MBOAT2 | MBOAT2 | 10682 | -0.022 | 0.27 | NO
327 | MTMR14 | MTMR14 | MTMR14 | 10767 | -0.023 | 0.27 | NO
328 | PPP1CB | PPP1CB | PPP1CB | 10797 | -0.023 | 0.26 | NO
329 | AMN | AMN | AMN | 10830 | -0.023 | 0.26 | NO
330 | LDLRAP1 | LDLRAP1 | LDLRAP1 | 10895 | -0.024 | 0.26 | NO
331 | PIK3R4 | PIK3R4 | PIK3R4 | 10926 | -0.025 | 0.26 | NO
332 | AGPAT1 | AGPAT1 | AGPAT1 | 10928 | -0.025 | 0.26 | NO
333 | FADS2 | FADS2 | FADS2 | 10935 | -0.025 | 0.26 | NO
334 | PIP4K2B | PIP4K2B | PIP4K2B | 11012 | -0.026 | 0.26 | NO
335 | NFYA | NFYA | NFYA | 11046 | -0.026 | 0.25 | NO
336 | TXNRD1 | TXNRD1 | TXNRD1 | 11066 | -0.026 | 0.25 | NO
337 | LPIN3 | LPIN3 | LPIN3 | 11196 | -0.028 | 0.25 | NO
338 | PGS1 | PGS1 | PGS1 | 11202 | -0.028 | 0.25 | NO
339 | MED7 | MED7 | MED7 | 11226 | -0.029 | 0.24 | NO
340 | MED12 | MED12 | MED12 | 11230 | -0.029 | 0.24 | NO
341 | FABP6 | FABP6 | FABP6 | 11291 | -0.03 | 0.24 | NO
342 | CDIPT | CDIPT | CDIPT | 11308 | -0.03 | 0.24 | NO
343 | CREBBP | CREBBP | CREBBP | 11359 | -0.03 | 0.24 | NO
344 | GBA2 | GBA2 | GBA2 | 11442 | -0.032 | 0.24 | NO
345 | CHKA | CHKA | CHKA | 11654 | -0.034 | 0.22 | NO
346 | SLC44A1 | SLC44A1 | SLC44A1 | 11674 | -0.034 | 0.22 | NO
347 | VAPA | VAPA | VAPA | 11697 | -0.035 | 0.22 | NO
348 | ABCD1 | ABCD1 | ABCD1 | 11742 | -0.035 | 0.22 | NO
349 | PTDSS1 | PTDSS1 | PTDSS1 | 11751 | -0.036 | 0.22 | NO
350 | PLA2G3 | PLA2G3 | PLA2G3 | 11892 | -0.037 | 0.21 | NO
351 | SIN3B | SIN3B | SIN3B | 11945 | -0.038 | 0.21 | NO
352 | ACOT8 | ACOT8 | ACOT8 | 11979 | -0.039 | 0.21 | NO
353 | PLA2G6 | PLA2G6 | PLA2G6 | 12065 | -0.04 | 0.2 | NO
354 | AGPAT6 | AGPAT6 | AGPAT6 | 12072 | -0.04 | 0.2 | NO
355 | LRP2 | LRP2 | LRP2 | 12213 | -0.042 | 0.2 | NO
356 | MED16 | MED16 | MED16 | 12225 | -0.042 | 0.2 | NO
357 | NEU3 | NEU3 | NEU3 | 12235 | -0.042 | 0.2 | NO
358 | SLC27A1 | SLC27A1 | SLC27A1 | 12327 | -0.044 | 0.19 | NO
359 | TBL1XR1 | TBL1XR1 | TBL1XR1 | 12414 | -0.045 | 0.19 | NO
360 | TECR | TECR | TECR | 12488 | -0.046 | 0.18 | NO
361 | GPAT2 | GPAT2 | GPAT2 | 12564 | -0.047 | 0.18 | NO
362 | FIG4 | FIG4 | FIG4 | 12570 | -0.047 | 0.18 | NO
363 | MED24 | MED24 | MED24 | 12650 | -0.049 | 0.18 | NO
364 | BMP1 | BMP1 | BMP1 | 12703 | -0.05 | 0.17 | NO
365 | INPPL1 | INPPL1 | INPPL1 | 12829 | -0.052 | 0.17 | NO
366 | SLC44A5 | SLC44A5 | SLC44A5 | 12850 | -0.052 | 0.17 | NO
367 | PLA2G4A | PLA2G4A | PLA2G4A | 12853 | -0.052 | 0.17 | NO
368 | PRIC285 | PRIC285 | PRIC285 | 12882 | -0.053 | 0.17 | NO
369 | PLD2 | PLD2 | PLD2 | 12907 | -0.053 | 0.16 | NO
370 | MED19 | MED19 | MED19 | 12960 | -0.054 | 0.16 | NO
371 | CTGF | CTGF | CTGF | 12990 | -0.054 | 0.16 | NO
372 | NCOA1 | NCOA1 | NCOA1 | 13130 | -0.056 | 0.16 | NO
373 | SMPD3 | SMPD3 | SMPD3 | 13138 | -0.056 | 0.16 | NO
374 | POMC | POMC | POMC | 13158 | -0.057 | 0.16 | NO
375 | MBOAT1 | MBOAT1 | MBOAT1 | 13173 | -0.057 | 0.16 | NO
376 | SPTLC1 | SPTLC1 | SPTLC1 | 13317 | -0.059 | 0.15 | NO
377 | ACSL4 | ACSL4 | ACSL4 | 13367 | -0.06 | 0.14 | NO
378 | PLA2G2F | PLA2G2F | PLA2G2F | 13499 | -0.063 | 0.14 | NO
379 | NRF1 | NRF1 | NRF1 | 13517 | -0.063 | 0.14 | NO
380 | DGAT1 | DGAT1 | DGAT1 | 13525 | -0.063 | 0.14 | NO
381 | SIN3A | SIN3A | SIN3A | 13572 | -0.064 | 0.14 | NO
382 | CYP19A1 | CYP19A1 | CYP19A1 | 13584 | -0.064 | 0.14 | NO
383 | PLA2G1B | PLA2G1B | PLA2G1B | 13703 | -0.066 | 0.13 | NO
384 | PPAP2C | PPAP2C | PPAP2C | 13738 | -0.067 | 0.13 | NO
385 | INPP4B | INPP4B | INPP4B | 13827 | -0.069 | 0.12 | NO
386 | CSNK1G2 | CSNK1G2 | CSNK1G2 | 13842 | -0.07 | 0.12 | NO
387 | SMPD2 | SMPD2 | SMPD2 | 13843 | -0.07 | 0.13 | NO
388 | WWTR1 | WWTR1 | WWTR1 | 13856 | -0.07 | 0.13 | NO
389 | AGPAT4 | AGPAT4 | AGPAT4 | 13864 | -0.07 | 0.13 | NO
390 | TEAD2 | TEAD2 | TEAD2 | 13980 | -0.072 | 0.12 | NO
391 | INPP5J | INPP5J | INPP5J | 13987 | -0.072 | 0.12 | NO
392 | PIP4K2A | PIP4K2A | PIP4K2A | 14116 | -0.075 | 0.12 | NO
393 | TGS1 | TGS1 | TGS1 | 14177 | -0.076 | 0.11 | NO
394 | LPCAT2 | LPCAT2 | LPCAT2 | 14205 | -0.077 | 0.11 | NO
395 | PIP5K1C | PIP5K1C | PIP5K1C | 14248 | -0.078 | 0.11 | NO
396 | PLD6 | PLD6 | PLD6 | 14272 | -0.078 | 0.11 | NO
397 | PCYT1B | PCYT1B | PCYT1B | 14331 | -0.08 | 0.11 | NO
398 | INPP5K | INPP5K | INPP5K | 14367 | -0.081 | 0.11 | NO
399 | LRAT | LRAT | LRAT | 14393 | -0.081 | 0.11 | NO
400 | TEAD3 | TEAD3 | TEAD3 | 14408 | -0.082 | 0.11 | NO
401 | TAZ | TAZ | TAZ | 14455 | -0.083 | 0.1 | NO
402 | PI4KB | PI4KB | PI4KB | 14458 | -0.083 | 0.1 | NO
403 | INPP5E | INPP5E | INPP5E | 14557 | -0.085 | 0.1 | NO
404 | TEAD4 | TEAD4 | TEAD4 | 14578 | -0.086 | 0.1 | NO
405 | FDFT1 | FDFT1 | FDFT1 | 14693 | -0.089 | 0.095 | NO
406 | ASAH1 | ASAH1 | ASAH1 | 14714 | -0.09 | 0.095 | NO
407 | STS | STS | STS | 14733 | -0.09 | 0.095 | NO
408 | PIK3CD | PIK3CD | PIK3CD | 14903 | -0.095 | 0.087 | NO
409 | GPD2 | GPD2 | GPD2 | 14977 | -0.097 | 0.084 | NO
410 | CHKB | CHKB | CHKB | 15028 | -0.098 | 0.082 | NO
411 | LHB | LHB | LHB | 15223 | -0.1 | 0.072 | NO
412 | MED21 | MED21 | MED21 | 15304 | -0.11 | 0.069 | NO
413 | MED27 | MED27 | MED27 | 15307 | -0.11 | 0.07 | NO
414 | PNPLA2 | PNPLA2 | PNPLA2 | 15336 | -0.11 | 0.07 | NO
415 | ACHE | ACHE | ACHE | 15521 | -0.12 | 0.061 | NO
416 | MED30 | MED30 | MED30 | 15546 | -0.12 | 0.06 | NO
417 | SRD5A3 | SRD5A3 | SRD5A3 | 15576 | -0.12 | 0.06 | NO
418 | MED17 | MED17 | MED17 | 15610 | -0.12 | 0.06 | NO
419 | MED22 | MED22 | MED22 | 15655 | -0.12 | 0.059 | NO
420 | PLD4 | PLD4 | PLD4 | 15678 | -0.12 | 0.059 | NO
421 | PTDSS2 | PTDSS2 | PTDSS2 | 15687 | -0.12 | 0.06 | NO
422 | TNFRSF21 | TNFRSF21 | TNFRSF21 | 15828 | -0.13 | 0.053 | NO
423 | LPL | LPL | LPL | 15982 | -0.13 | 0.046 | NO
424 | GPCPD1 | GPCPD1 | GPCPD1 | 16178 | -0.14 | 0.037 | NO
425 | PLBD1 | PLBD1 | PLBD1 | 16197 | -0.15 | 0.037 | NO
426 | CYP24A1 | CYP24A1 | CYP24A1 | 16240 | -0.15 | 0.037 | NO
427 | LPCAT4 | LPCAT4 | LPCAT4 | 16247 | -0.15 | 0.038 | NO
428 | MTMR2 | MTMR2 | MTMR2 | 16253 | -0.15 | 0.04 | NO
429 | MED20 | MED20 | MED20 | 16432 | -0.16 | 0.031 | NO
430 | PLA2G4F | PLA2G4F | PLA2G4F | 16488 | -0.16 | 0.03 | NO
431 | SPHK1 | SPHK1 | SPHK1 | 16527 | -0.17 | 0.03 | NO
432 | CAV1 | CAV1 | CAV1 | 16666 | -0.18 | 0.024 | NO
433 | ABCG1 | ABCG1 | ABCG1 | 16790 | -0.19 | 0.019 | NO
434 | CUBN | CUBN | CUBN | 16807 | -0.19 | 0.02 | NO
435 | HSD3B2 | HSD3B2 | HSD3B2 | 16823 | -0.19 | 0.022 | NO
436 | PIP5K1B | PIP5K1B | PIP5K1B | 16860 | -0.19 | 0.022 | NO
437 | PLA2G10 | PLA2G10 | PLA2G10 | 16940 | -0.2 | 0.02 | NO
438 | STAR | STAR | STAR | 16974 | -0.21 | 0.02 | NO
439 | NR1D1 | NR1D1 | NR1D1 | 17067 | -0.22 | 0.018 | NO
440 | ELOVL4 | ELOVL4 | ELOVL4 | 17172 | -0.23 | 0.014 | NO
441 | SGPP2 | SGPP2 | SGPP2 | 17209 | -0.23 | 0.015 | NO
442 | OXCT1 | OXCT1 | OXCT1 | 17213 | -0.23 | 0.017 | NO
443 | RBP2 | RBP2 | RBP2 | 17263 | -0.24 | 0.017 | NO
444 | SMARCD3 | SMARCD3 | SMARCD3 | 17338 | -0.24 | 0.016 | NO
445 | PLA2G4D | PLA2G4D | PLA2G4D | 17437 | -0.26 | 0.013 | NO
446 | SLC10A2 | SLC10A2 | SLC10A2 | 17447 | -0.26 | 0.016 | NO
447 | DEGS2 | DEGS2 | DEGS2 | 17527 | -0.28 | 0.014 | NO
448 | PIK3R6 | PIK3R6 | PIK3R6 | 17568 | -0.28 | 0.016 | NO
449 | TPTE2 | TPTE2 | TPTE2 | 17683 | -0.31 | 0.013 | NO
450 | ARSH | ARSH | ARSH | 17758 | -0.33 | 0.012 | NO
451 | LIPE | LIPE | LIPE | 17826 | -0.34 | 0.012 | NO
452 | SLC44A4 | SLC44A4 | SLC44A4 | 17831 | -0.35 | 0.016 | NO

Figure S83. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CITRATE CYCLE TCA CYCLE.

Figure S84. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CITRATE CYCLE TCA CYCLE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PENTOSE PHOSPHATE PATHWAY

Table S43. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | SULT2A1 | SULT2A1 | SULT2A1 | 26 | 2 | 0.061 | YES
2 | APOA5 | APOA5 | APOA5 | 29 | 1.9 | 0.12 | YES
3 | APOA1 | APOA1 | APOA1 | 83 | 1.5 | 0.17 | YES
4 | FABP1 | FABP1 | FABP1 | 121 | 1.3 | 0.21 | YES
5 | ABCB4 | ABCB4 | ABCB4 | 142 | 1.2 | 0.24 | YES
6 | CYP7A1 | CYP7A1 | CYP7A1 | 144 | 1.2 | 0.28 | YES
7 | CYP1A1 | CYP1A1 | CYP1A1 | 154 | 1.1 | 0.32 | YES
8 | APOA2 | APOA2 | APOA2 | 155 | 1.1 | 0.35 | YES
9 | HMGCS2 | HMGCS2 | HMGCS2 | 175 | 1 | 0.39 | YES
10 | CYP4A11 | CYP4A11 | CYP4A11 | 239 | 0.83 | 0.41 | YES
11 | GPD1 | GPD1 | GPD1 | 273 | 0.77 | 0.43 | YES
12 | ACADL | ACADL | ACADL | 288 | 0.72 | 0.46 | YES
13 | BDH1 | BDH1 | BDH1 | 330 | 0.66 | 0.47 | YES
14 | GPAM | GPAM | GPAM | 356 | 0.61 | 0.49 | YES
15 | DGAT2 | DGAT2 | DGAT2 | 386 | 0.57 | 0.51 | YES
16 | G0S2 | G0S2 | G0S2 | 435 | 0.52 | 0.52 | YES
17 | ACSL1 | ACSL1 | ACSL1 | 473 | 0.49 | 0.54 | YES
18 | ELOVL2 | ELOVL2 | ELOVL2 | 502 | 0.47 | 0.55 | YES
19 | UGT1A9 | UGT1A9 | UGT1A9 | 562 | 0.43 | 0.56 | YES
20 | CD36 | CD36 | CD36 | 651 | 0.38 | 0.57 | YES
21 | PLIN2 | PLIN2 | PLIN2 | 655 | 0.38 | 0.58 | YES
22 | ANGPTL4 | ANGPTL4 | ANGPTL4 | 805 | 0.33 | 0.58 | YES
23 | ACSL6 | ACSL6 | ACSL6 | 864 | 0.31 | 0.59 | YES
24 | ELOVL6 | ELOVL6 | ELOVL6 | 972 | 0.28 | 0.59 | YES
25 | SLC25A20 | SLC25A20 | SLC25A20 | 1026 | 0.27 | 0.6 | YES
26 | ANKRD1 | ANKRD1 | ANKRD1 | 1135 | 0.26 | 0.6 | YES
27 | AGT | AGT | AGT | 1136 | 0.26 | 0.61 | YES
28 | MCEE | MCEE | MCEE | 1162 | 0.25 | 0.61 | YES
29 | ACAT1 | ACAT1 | ACAT1 | 1163 | 0.25 | 0.62 | YES
30 | ACSL5 | ACSL5 | ACSL5 | 1246 | 0.24 | 0.62 | YES
31 | ELOVL7 | ELOVL7 | ELOVL7 | 1369 | 0.22 | 0.62 | YES
32 | ALAS1 | ALAS1 | ALAS1 | 1388 | 0.22 | 0.63 | YES
33 | HMGCS1 | HMGCS1 | HMGCS1 | 1538 | 0.2 | 0.63 | YES
34 | FASN | FASN | FASN | 1623 | 0.19 | 0.63 | YES
35 | ABCA1 | ABCA1 | ABCA1 | 1641 | 0.19 | 0.64 | YES
36 | HMGCL | HMGCL | HMGCL | 1756 | 0.18 | 0.63 | YES
37 | ACACB | ACACB | ACACB | 1791 | 0.18 | 0.64 | YES
38 | ACADM | ACADM | ACADM | 1865 | 0.17 | 0.64 | YES
39 | CPT2 | CPT2 | CPT2 | 1964 | 0.16 | 0.64 | YES
40 | PPARA | PPARA | PPARA | 1990 | 0.16 | 0.64 | YES
41 | ACOX1 | ACOX1 | ACOX1 | 2024 | 0.16 | 0.65 | YES
42 | PRKAA2 | PRKAA2 | PRKAA2 | 2091 | 0.16 | 0.65 | YES
43 | ECHS1 | ECHS1 | ECHS1 | 2114 | 0.15 | 0.65 | YES
44 | ELOVL3 | ELOVL3 | ELOVL3 | 2155 | 0.15 | 0.65 | YES
45 | ARNTL | ARNTL | ARNTL | 2245 | 0.15 | 0.65 | YES
46 | GRHL1 | GRHL1 | GRHL1 | 2312 | 0.14 | 0.65 | YES
47 | TRIB3 | TRIB3 | TRIB3 | 2442 | 0.14 | 0.65 | YES
48 | MUT | MUT | MUT | 2466 | 0.13 | 0.65 | YES
49 | ACADS | ACADS | ACADS | 2519 | 0.13 | 0.66 | YES
50 | ELOVL5 | ELOVL5 | ELOVL5 | 2884 | 0.11 | 0.64 | NO
51 | MED8 | MED8 | MED8 | 3004 | 0.11 | 0.64 | NO
52 | HMGCR | HMGCR | HMGCR | 3112 | 0.1 | 0.63 | NO
53 | FADS1 | FADS1 | FADS1 | 3220 | 0.099 | 0.63 | NO
54 | NPAS2 | NPAS2 | NPAS2 | 3223 | 0.099 | 0.63 | NO
55 | MED31 | MED31 | MED31 | 3416 | 0.094 | 0.63 | NO
56 | ACADVL | ACADVL | ACADVL | 3459 | 0.092 | 0.63 | NO
57 | CCNC | CCNC | CCNC | 3705 | 0.085 | 0.62 | NO
58 | ELOVL1 | ELOVL1 | ELOVL1 | 3744 | 0.084 | 0.62 | NO
59 | NCOA2 | NCOA2 | NCOA2 | 3791 | 0.083 | 0.62 | NO
60 | ACSL3 | ACSL3 | ACSL3 | 4014 | 0.076 | 0.61 | NO
61 | HADHB | HADHB | HADHB | 4022 | 0.076 | 0.61 | NO
62 | SREBF2 | SREBF2 | SREBF2 | 4155 | 0.073 | 0.6 | NO
63 | PPARGC1B | PPARGC1B | PPARGC1B | 4367 | 0.068 | 0.59 | NO
64 | AGPAT3 | AGPAT3 | AGPAT3 | 4456 | 0.065 | 0.59 | NO
65 | PPARGC1A | PPARGC1A | PPARGC1A | 4518 | 0.064 | 0.59 | NO
66 | LPIN2 | LPIN2 | LPIN2 | 4590 | 0.062 | 0.59 | NO
67 | EP300 | EP300 | EP300 | 4615 | 0.062 | 0.59 | NO
68 | HADH | HADH | HADH | 4896 | 0.056 | 0.57 | NO
69 | PEX11A | PEX11A | PEX11A | 4914 | 0.055 | 0.57 | NO
70 | PRKAG2 | PRKAG2 | PRKAG2 | 5014 | 0.053 | 0.57 | NO
71 | TIAM2 | TIAM2 | TIAM2 | 5094 | 0.052 | 0.57 | NO
72 | GK | GK | GK | 5111 | 0.052 | 0.57 | NO
73 | HSD17B12 | HSD17B12 | HSD17B12 | 5120 | 0.051 | 0.57 | NO
74 | HADHA | HADHA | HADHA | 5144 | 0.051 | 0.57 | NO
75 | GPD1L | GPD1L | GPD1L | 5179 | 0.05 | 0.57 | NO
76 | PCCB | PCCB | PCCB | 5362 | 0.047 | 0.56 | NO
77 | CPT1A | CPT1A | CPT1A | 5540 | 0.043 | 0.55 | NO
78 | AGPAT9 | AGPAT9 | AGPAT9 | 5549 | 0.043 | 0.55 | NO
79 | PRKAB2 | PRKAB2 | PRKAB2 | 5699 | 0.04 | 0.55 | NO
80 | SREBF1 | SREBF1 | SREBF1 | 5824 | 0.038 | 0.54 | NO
81 | MED23 | MED23 | MED23 | 5963 | 0.036 | 0.54 | NO
82 | LCLAT1 | LCLAT1 | LCLAT1 | 6052 | 0.035 | 0.53 | NO
83 | CDK8 | CDK8 | CDK8 | 6256 | 0.032 | 0.52 | NO
84 | ESRRA | ESRRA | ESRRA | 6409 | 0.03 | 0.51 | NO
85 | MED29 | MED29 | MED29 | 6459 | 0.029 | 0.51 | NO
86 | MED10 | MED10 | MED10 | 6523 | 0.028 | 0.51 | NO
87 | ME1 | ME1 | ME1 | 6698 | 0.026 | 0.5 | NO
88 | PCCA | PCCA | PCCA | 6736 | 0.026 | 0.5 | NO
89 | TEAD1 | TEAD1 | TEAD1 | 6893 | 0.024 | 0.49 | NO
90 | LPCAT1 | LPCAT1 | LPCAT1 | 6930 | 0.023 | 0.49 | NO
91 | CDK19 | CDK19 | CDK19 | 6987 | 0.022 | 0.49 | NO
92 | RXRA | RXRA | RXRA | 7058 | 0.021 | 0.48 | NO
93 | NFYB | NFYB | NFYB | 7150 | 0.02 | 0.48 | NO
94 | ACLY | ACLY | ACLY | 7156 | 0.02 | 0.48 | NO
95 | ACACA | ACACA | ACACA | 7181 | 0.02 | 0.48 | NO
96 | LPIN1 | LPIN1 | LPIN1 | 7412 | 0.017 | 0.47 | NO
97 | NCOA3 | NCOA3 | NCOA3 | 7449 | 0.016 | 0.46 | NO
98 | MED11 | MED11 | MED11 | 7594 | 0.014 | 0.46 | NO
99 | SLC25A1 | SLC25A1 | SLC25A1 | 7615 | 0.014 | 0.46 | NO
100 | TBL1X | TBL1X | TBL1X | 7812 | 0.012 | 0.45 | NO
101 | PPARG | PPARG | PPARG | 8013 | 0.0092 | 0.44 | NO
102 | CPT1B | CPT1B | CPT1B | 8122 | 0.0081 | 0.43 | NO
103 | HDAC3 | HDAC3 | HDAC3 | 8129 | 0.008 | 0.43 | NO
104 | RORA | RORA | RORA | 8204 | 0.007 | 0.43 | NO
105 | AGPAT5 | AGPAT5 | AGPAT5 | 8739 | 0.00072 | 0.4 | NO
106 | NCOR2 | NCOR2 | NCOR2 | 8825 | -0.00015 | 0.39 | NO
107 | MED9 | MED9 | MED9 | 8990 | -0.0021 | 0.38 | NO
108 | GLIPR1 | GLIPR1 | GLIPR1 | 9568 | -0.0085 | 0.35 | NO
109 | FHL2 | FHL2 | FHL2 | 9647 | -0.0095 | 0.35 | NO
110 | MED1 | MED1 | MED1 | 9875 | -0.012 | 0.33 | NO
111 | MED25 | MED25 | MED25 | 9885 | -0.012 | 0.33 | NO
112 | MED6 | MED6 | MED6 | 9947 | -0.013 | 0.33 | NO
113 | YAP1 | YAP1 | YAP1 | 10003 | -0.013 | 0.33 | NO
114 | AGPAT2 | AGPAT2 | AGPAT2 | 10079 | -0.014 | 0.32 | NO
115 | MED13L | MED13L | MED13L | 10117 | -0.015 | 0.32 | NO
116 | MED26 | MED26 | MED26 | 10151 | -0.015 | 0.32 | NO
117 | NCOR1 | NCOR1 | NCOR1 | 10218 | -0.016 | 0.32 | NO
118 | MED14 | MED14 | MED14 | 10229 | -0.016 | 0.32 | NO
119 | MED4 | MED4 | MED4 | 10281 | -0.017 | 0.32 | NO
120 | MED18 | MED18 | MED18 | 10438 | -0.019 | 0.31 | NO
121 | NCOA6 | NCOA6 | NCOA6 | 10527 | -0.02 | 0.3 | NO
122 | DECR1 | DECR1 | DECR1 | 10540 | -0.02 | 0.3 | NO
123 | MED15 | MED15 | MED15 | 10546 | -0.02 | 0.3 | NO
124 | CLOCK | CLOCK | CLOCK | 10649 | -0.021 | 0.3 | NO
125 | AGPAT1 | AGPAT1 | AGPAT1 | 10928 | -0.025 | 0.28 | NO
126 | NFYA | NFYA | NFYA | 11046 | -0.026 | 0.28 | NO
127 | TXNRD1 | TXNRD1 | TXNRD1 | 11066 | -0.026 | 0.28 | NO
128 | LPIN3 | LPIN3 | LPIN3 | 11196 | -0.028 | 0.27 | NO
129 | MED7 | MED7 | MED7 | 11226 | -0.029 | 0.27 | NO
130 | MED12 | MED12 | MED12 | 11230 | -0.029 | 0.27 | NO
131 | CREBBP | CREBBP | CREBBP | 11359 | -0.03 | 0.27 | NO
132 | SIN3B | SIN3B | SIN3B | 11945 | -0.038 | 0.24 | NO
133 | AGPAT6 | AGPAT6 | AGPAT6 | 12072 | -0.04 | 0.23 | NO
134 | MED16 | MED16 | MED16 | 12225 | -0.042 | 0.22 | NO
135 | SLC27A1 | SLC27A1 | SLC27A1 | 12327 | -0.044 | 0.22 | NO
136 | TBL1XR1 | TBL1XR1 | TBL1XR1 | 12414 | -0.045 | 0.21 | NO
137 | TECR | TECR | TECR | 12488 | -0.046 | 0.21 | NO
138 | GPAT2 | GPAT2 | GPAT2 | 12564 | -0.047 | 0.21 | NO
139 | MED24 | MED24 | MED24 | 12650 | -0.049 | 0.21 | NO
140 | PRIC285 | PRIC285 | PRIC285 | 12882 | -0.053 | 0.2 | NO
141 | MED19 | MED19 | MED19 | 12960 | -0.054 | 0.19 | NO
142 | CTGF | CTGF | CTGF | 12990 | -0.054 | 0.19 | NO
143 | NCOA1 | NCOA1 | NCOA1 | 13130 | -0.056 | 0.19 | NO
144 | ACSL4 | ACSL4 | ACSL4 | 13367 | -0.06 | 0.18 | NO
145 | NRF1 | NRF1 | NRF1 | 13517 | -0.063 | 0.17 | NO
146 | DGAT1 | DGAT1 | DGAT1 | 13525 | -0.063 | 0.17 | NO
147 | SIN3A | SIN3A | SIN3A | 13572 | -0.064 | 0.17 | NO
148 | WWTR1 | WWTR1 | WWTR1 | 13856 | -0.07 | 0.16 | NO
149 | AGPAT4 | AGPAT4 | AGPAT4 | 13864 | -0.07 | 0.16 | NO
150 | TEAD2 | TEAD2 | TEAD2 | 13980 | -0.072 | 0.15 | NO
151 | TGS1 | TGS1 | TGS1 | 14177 | -0.076 | 0.15 | NO
152 | TEAD3 | TEAD3 | TEAD3 | 14408 | -0.082 | 0.14 | NO
153 | TEAD4 | TEAD4 | TEAD4 | 14578 | -0.086 | 0.13 | NO
154 | FDFT1 | FDFT1 | FDFT1 | 14693 | -0.089 | 0.12 | NO
155 | GPD2 | GPD2 | GPD2 | 14977 | -0.097 | 0.11 | NO
156 | MED21 | MED21 | MED21 | 15304 | -0.11 | 0.098 | NO
157 | MED27 | MED27 | MED27 | 15307 | -0.11 | 0.1 | NO
158 | MED30 | MED30 | MED30 | 15546 | -0.12 | 0.092 | NO
159 | MED17 | MED17 | MED17 | 15610 | -0.12 | 0.092 | NO
160 | MED22 | MED22 | MED22 | 15655 | -0.12 | 0.093 | NO
161 | TNFRSF21 | TNFRSF21 | TNFRSF21 | 15828 | -0.13 | 0.088 | NO
162 | LPCAT4 | LPCAT4 | LPCAT4 | 16247 | -0.15 | 0.069 | NO
163 | MED20 | MED20 | MED20 | 16432 | -0.16 | 0.064 | NO
164 | NR1D1 | NR1D1 | NR1D1 | 17067 | -0.22 | 0.036 | NO
165 | ELOVL4 | ELOVL4 | ELOVL4 | 17172 | -0.23 | 0.037 | NO
166 | OXCT1 | OXCT1 | OXCT1 | 17213 | -0.23 | 0.042 | NO
167 | SMARCD3 | SMARCD3 | SMARCD3 | 17338 | -0.24 | 0.043 | NO

Figure S85. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PENTOSE PHOSPHATE PATHWAY.

Figure S86. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PENTOSE PHOSPHATE PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS

Table S44. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | HAO1 | HAO1 | HAO1 | 5 | 2.3 | 0.044 | YES
2 | ARG1 | ARG1 | ARG1 | 12 | 2.1 | 0.085 | YES
3 | UROC1 | UROC1 | UROC1 | 16 | 2.1 | 0.12 | YES
4 | TAT | TAT | TAT | 27 | 1.9 | 0.16 | YES
5 | CPS1 | CPS1 | CPS1 | 38 | 1.8 | 0.2 | YES
6 | OTC | OTC | OTC | 46 | 1.8 | 0.23 | YES
7 | DAO | DAO | DAO | 58 | 1.7 | 0.26 | YES
8 | AGXT | AGXT | AGXT | 59 | 1.7 | 0.3 | YES
9 | BHMT | BHMT | BHMT | 60 | 1.7 | 0.33 | YES
10 | CDO1 | CDO1 | CDO1 | 67 | 1.6 | 0.36 | YES
11 | INHBC | INHBC | INHBC | 137 | 1.2 | 0.38 | YES
12 | TDO2 | TDO2 | TDO2 | 138 | 1.2 | 0.4 | YES
13 | HPD | HPD | HPD | 157 | 1.1 | 0.42 | YES
14 | AGXT2 | AGXT2 | AGXT2 | 170 | 1.1 | 0.44 | YES
15 | MAT1A | MAT1A | MAT1A | 190 | 1 | 0.46 | YES
16 | AMDHD1 | AMDHD1 | AMDHD1 | 193 | 0.99 | 0.48 | YES
17 | HAL | HAL | HAL | 197 | 0.99 | 0.5 | YES
18 | DIO1 | DIO1 | DIO1 | 213 | 0.93 | 0.52 | YES
19 | DBH | DBH | DBH | 214 | 0.92 | 0.53 | YES
20 | KMO | KMO | KMO | 228 | 0.87 | 0.55 | YES
21 | GLS2 | GLS2 | GLS2 | 263 | 0.8 | 0.56 | YES
22 | FTCD | FTCD | FTCD | 286 | 0.73 | 0.58 | YES
23 | CTH | CTH | CTH | 318 | 0.67 | 0.59 | YES
24 | DDC | DDC | DDC | 375 | 0.58 | 0.6 | YES
25 | INHBE | INHBE | INHBE | 391 | 0.56 | 0.61 | YES
26 | PSAT1 | PSAT1 | PSAT1 | 397 | 0.56 | 0.62 | YES
27 | IDO2 | IDO2 | IDO2 | 414 | 0.54 | 0.63 | YES
28 | GPT2 | GPT2 | GPT2 | 448 | 0.51 | 0.64 | YES
29 | KYNU | KYNU | KYNU | 462 | 0.5 | 0.64 | YES
30 | ALDH6A1 | ALDH6A1 | ALDH6A1 | 477 | 0.48 | 0.65 | YES
31 | AGMAT | AGMAT | AGMAT | 516 | 0.46 | 0.66 | YES
32 | NAGS | NAGS | NAGS | 531 | 0.45 | 0.67 | YES
33 | PAH | PAH | PAH | 532 | 0.45 | 0.68 | YES
34 | HAAO | HAAO | HAAO | 555 | 0.43 | 0.68 | YES
35 | ACADSB | ACADSB | ACADSB | 612 | 0.4 | 0.69 | YES
36 | IYD | IYD | IYD | 705 | 0.36 | 0.69 | YES
37 | GAMT | GAMT | GAMT | 720 | 0.35 | 0.7 | YES
38 | GATM | GATM | GATM | 731 | 0.35 | 0.7 | YES
39 | CBS | CBS | CBS | 739 | 0.34 | 0.71 | YES
40 | SLC25A15 | SLC25A15 | SLC25A15 | 787 | 0.33 | 0.71 | YES
41 | GPT | GPT | GPT | 810 | 0.32 | 0.72 | YES
42 | ALDH4A1 | ALDH4A1 | ALDH4A1 | 902 | 0.3 | 0.72 | YES
43 | BCKDHB | BCKDHB | BCKDHB | 915 | 0.3 | 0.72 | YES
44 | AADAT | AADAT | AADAT | 927 | 0.3 | 0.73 | YES
45 | ACMSD | ACMSD | ACMSD | 939 | 0.29 | 0.73 | YES
46 | FAH | FAH | FAH | 955 | 0.29 | 0.74 | YES
47 | SHMT1 | SHMT1 | SHMT1 | 1093 | 0.26 | 0.74 | YES
48 | ACAT1 | ACAT1 | ACAT1 | 1163 | 0.25 | 0.74 | YES
49 | PRODH | PRODH | PRODH | 1258 | 0.24 | 0.74 | YES
50 | HGD | HGD | HGD | 1261 | 0.24 | 0.74 | YES
51 | TST | TST | TST | 1287 | 0.23 | 0.74 | YES
52 | AANAT | AANAT | AANAT | 1443 | 0.21 | 0.74 | YES
53 | AASS | AASS | AASS | 1471 | 0.21 | 0.74 | YES
54 | PYCR1 | PYCR1 | PYCR1 | 1510 | 0.2 | 0.74 | YES
55 | GOT1 | GOT1 | GOT1 | 1532 | 0.2 | 0.75 | YES
56 | PSPH | PSPH | PSPH | 1633 | 0.19 | 0.74 | NO
57 | GSTZ1 | GSTZ1 | GSTZ1 | 1752 | 0.18 | 0.74 | NO
58 | CKMT2 | CKMT2 | CKMT2 | 1798 | 0.18 | 0.74 | NO
59 | SLC25A10 | SLC25A10 | SLC25A10 | 1832 | 0.17 | 0.74 | NO
60 | GOT2 | GOT2 | GOT2 | 1968 | 0.16 | 0.74 | NO
61 | ASL | ASL | ASL | 2040 | 0.16 | 0.74 | NO
62 | PHGDH | PHGDH | PHGDH | 2050 | 0.16 | 0.74 | NO
63 | QDPR | QDPR | QDPR | 2071 | 0.16 | 0.74 | NO
64 | AFMID | AFMID | AFMID | 2437 | 0.14 | 0.72 | NO
65 | GRHPR | GRHPR | GRHPR | 2469 | 0.13 | 0.73 | NO
66 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 2555 | 0.13 | 0.72 | NO
67 | HIBADH | HIBADH | HIBADH | 2789 | 0.12 | 0.71 | NO
68 | CKB | CKB | CKB | 3022 | 0.11 | 0.7 | NO
69 | CSAD | CSAD | CSAD | 3071 | 0.1 | 0.7 | NO
70 | ASS1 | ASS1 | ASS1 | 3145 | 0.1 | 0.7 | NO
71 | PAOX | PAOX | PAOX | 3189 | 0.1 | 0.7 | NO
72 | ADI1 | ADI1 | ADI1 | 3269 | 0.098 | 0.7 | NO
73 | PCBD1 | PCBD1 | PCBD1 | 3296 | 0.096 | 0.7 | NO
74 | HIBCH | HIBCH | HIBCH | 3632 | 0.087 | 0.68 | NO
75 | GLUD1 | GLUD1 | GLUD1 | 3722 | 0.085 | 0.68 | NO
76 | PSMD12 | PSMD12 | PSMD12 | 3730 | 0.084 | 0.68 | NO
77 | OAT | OAT | OAT | 3863 | 0.08 | 0.67 | NO
78 | HDC | HDC | HDC | 3961 | 0.078 | 0.67 | NO
79 | MCCC2 | MCCC2 | MCCC2 | 3962 | 0.078 | 0.67 | NO
80 | IVD | IVD | IVD | 3974 | 0.077 | 0.67 | NO
81 | CNDP2 | CNDP2 | CNDP2 | 4032 | 0.076 | 0.67 | NO
82 | CKM | CKM | CKM | 4130 | 0.074 | 0.66 | NO
83 | PSMD11 | PSMD11 | PSMD11 | 4256 | 0.07 | 0.66 | NO
84 | GCLC | GCLC | GCLC | 4371 | 0.068 | 0.65 | NO
85 | PSMC4 | PSMC4 | PSMC4 | 4427 | 0.066 | 0.65 | NO
86 | SUOX | SUOX | SUOX | 4440 | 0.066 | 0.65 | NO
87 | BCKDHA | BCKDHA | BCKDHA | 4442 | 0.066 | 0.65 | NO
88 | PSMC2 | PSMC2 | PSMC2 | 4473 | 0.065 | 0.65 | NO
89 | AHCY | AHCY | AHCY | 4629 | 0.062 | 0.65 | NO
90 | ODC1 | ODC1 | ODC1 | 4655 | 0.061 | 0.65 | NO
91 | SLC25A21 | SLC25A21 | SLC25A21 | 4691 | 0.06 | 0.64 | NO
92 | ALDH18A1 | ALDH18A1 | ALDH18A1 | 4798 | 0.058 | 0.64 | NO
93 | DLD | DLD | DLD | 4899 | 0.056 | 0.64 | NO
94 | MAT2A | MAT2A | MAT2A | 5257 | 0.049 | 0.62 | NO
95 | SLC25A2 | SLC25A2 | SLC25A2 | 5335 | 0.047 | 0.61 | NO
96 | PSMC6 | PSMC6 | PSMC6 | 5448 | 0.045 | 0.61 | NO
97 | SLC5A5 | SLC5A5 | SLC5A5 | 5464 | 0.044 | 0.61 | NO
98 | GCDH | GCDH | GCDH | 5503 | 0.044 | 0.61 | NO
99 | ARG2 | ARG2 | ARG2 | 5534 | 0.043 | 0.61 | NO
100 | PSMA2 | PSMA2 | PSMA2 | 5536 | 0.043 | 0.61 | NO
101 | DBT | DBT | DBT | 5547 | 0.043 | 0.61 | NO
102 | PSMD6 | PSMD6 | PSMD6 | 5548 | 0.043 | 0.61 | NO
103 | PSMB5 | PSMB5 | PSMB5 | 5673 | 0.041 | 0.6 | NO
104 | DIO3 | DIO3 | DIO3 | 5685 | 0.04 | 0.6 | NO
105 | MTAP | MTAP | MTAP | 5801 | 0.038 | 0.6 | NO
106 | PSMC5 | PSMC5 | PSMC5 | 5811 | 0.038 | 0.6 | NO
107 | PSME4 | PSME4 | PSME4 | 5845 | 0.038 | 0.6 | NO
108 | DLST | DLST | DLST | 5883 | 0.037 | 0.59 | NO
109 | PSMA3 | PSMA3 | PSMA3 | 5942 | 0.036 | 0.59 | NO
110 | INHBB | INHBB | INHBB | 6054 | 0.035 | 0.59 | NO
111 | PSMD8 | PSMD8 | PSMD8 | 6278 | 0.032 | 0.57 | NO
112 | PSMD10 | PSMD10 | PSMD10 | 6337 | 0.031 | 0.57 | NO
113 | PSMA5 | PSMA5 | PSMA5 | 6445 | 0.03 | 0.57 | NO
114 | PSMD2 | PSMD2 | PSMD2 | 6532 | 0.028 | 0.56 | NO
115 | PSMA6 | PSMA6 | PSMA6 | 6553 | 0.028 | 0.56 | NO
116 | ASNS | ASNS | ASNS | 6829 | 0.025 | 0.55 | NO
117 | PSMD14 | PSMD14 | PSMD14 | 6914 | 0.023 | 0.54 | NO
118 | PSMD1 | PSMD1 | PSMD1 | 6960 | 0.023 | 0.54 | NO
119 | PSMF1 | PSMF1 | PSMF1 | 7131 | 0.02 | 0.53 | NO
120 | OAZ2 | OAZ2 | OAZ2 | 7151 | 0.02 | 0.53 | NO
121 | HSD17B10 | HSD17B10 | HSD17B10 | 7193 | 0.019 | 0.53 | NO
122 | PSMD3 | PSMD3 | PSMD3 | 7324 | 0.018 | 0.52 | NO
123 | OGDH | OGDH | OGDH | 7415 | 0.016 | 0.52 | NO
124 | ETHE1 | ETHE1 | ETHE1 | 7503 | 0.015 | 0.51 | NO
125 | MTR | MTR | MTR | 7532 | 0.015 | 0.51 | NO
126 | PSME2 | PSME2 | PSME2 | 7543 | 0.015 | 0.51 | NO
127 | MAT2B | MAT2B | MAT2B | 7683 | 0.013 | 0.5 | NO
128 | PSMD7 | PSMD7 | PSMD7 | 7928 | 0.01 | 0.49 | NO
129 | PSMD9 | PSMD9 | PSMD9 | 7959 | 0.0099 | 0.49 | NO
130 | TMLHE | TMLHE | TMLHE | 8132 | 0.008 | 0.48 | NO
131 | PSMB3 | PSMB3 | PSMB3 | 8190 | 0.0072 | 0.48 | NO
132 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 8254 | 0.0064 | 0.47 | NO
133 | BBOX1 | BBOX1 | BBOX1 | 8353 | 0.0051 | 0.47 | NO
134 | PSME1 | PSME1 | PSME1 | 8385 | 0.0048 | 0.47 | NO
135 | SRM | SRM | SRM | 8631 | 0.0018 | 0.45 | NO
136 | AUH | AUH | AUH | 8738 | 0.00072 | 0.45 | NO
137 | NQO1 | NQO1 | NQO1 | 9047 | -0.0027 | 0.43 | NO
138 | PSMB6 | PSMB6 | PSMB6 | 9089 | -0.0031 | 0.43 | NO
139 | CGA | CGA | CGA | 9155 | -0.0039 | 0.42 | NO
140 | MCCC1 | MCCC1 | MCCC1 | 9161 | -0.004 | 0.42 | NO
141 | SQRDL | SQRDL | SQRDL | 9197 | -0.0044 | 0.42 | NO
142 | AMD1 | AMD1 | AMD1 | 9570 | -0.0085 | 0.4 | NO
143 | GLS | GLS | GLS | 9778 | -0.011 | 0.39 | NO
144 | GLUL | GLUL | GLUL | 9813 | -0.011 | 0.39 | NO
145 | AZIN1 | AZIN1 | AZIN1 | 9835 | -0.012 | 0.39 | NO
146 | GCLM | GCLM | GCLM | 9985 | -0.013 | 0.38 | NO
147 | TH | TH | TH | 10134 | -0.015 | 0.37 | NO
148 | PSMA1 | PSMA1 | PSMA1 | 10179 | -0.016 | 0.37 | NO
149 | TPH1 | TPH1 | TPH1 | 10293 | -0.017 | 0.36 | NO
150 | PSMB4 | PSMB4 | PSMB4 | 10693 | -0.022 | 0.34 | NO
151 | PSMB7 | PSMB7 | PSMB7 | 10877 | -0.024 | 0.33 | NO
152 | PSMB2 | PSMB2 | PSMB2 | 10893 | -0.024 | 0.33 | NO
153 | PSMA7 | PSMA7 | PSMA7 | 11015 | -0.026 | 0.32 | NO
154 | SMS | SMS | SMS | 11054 | -0.026 | 0.32 | NO
155 | OAZ1 | OAZ1 | OAZ1 | 11068 | -0.026 | 0.32 | NO
156 | PSMB1 | PSMB1 | PSMB1 | 11076 | -0.027 | 0.32 | NO
157 | INHBA | INHBA | INHBA | 11329 | -0.03 | 0.31 | NO
158 | PSMD5 | PSMD5 | PSMD5 | 11587 | -0.033 | 0.3 | NO
159 | PSMD4 | PSMD4 | PSMD4 | 11635 | -0.034 | 0.29 | NO
160 | OAZ3 | OAZ3 | OAZ3 | 11637 | -0.034 | 0.29 | NO
161 | ACAD8 | ACAD8 | ACAD8 | 11741 | -0.035 | 0.29 | NO
162 | PSMA4 | PSMA4 | PSMA4 | 11850 | -0.037 | 0.28 | NO
163 | PSMC1 | PSMC1 | PSMC1 | 11902 | -0.038 | 0.28 | NO
164 | DIO2 | DIO2 | DIO2 | 12446 | -0.046 | 0.25 | NO
165 | PSMC3 | PSMC3 | PSMC3 | 12563 | -0.047 | 0.25 | NO
166 | PSMB8 | PSMB8 | PSMB8 | 12814 | -0.051 | 0.23 | NO
167 | CCBL1 | CCBL1 | CCBL1 | 12832 | -0.052 | 0.23 | NO
168 | PSMB9 | PSMB9 | PSMB9 | 12886 | -0.053 | 0.23 | NO
169 | POMC | POMC | POMC | 13158 | -0.057 | 0.22 | NO
170 | SAT1 | SAT1 | SAT1 | 13228 | -0.058 | 0.22 | NO
171 | INHA | INHA | INHA | 13232 | -0.058 | 0.22 | NO
172 | ENOPH1 | ENOPH1 | ENOPH1 | 13723 | -0.067 | 0.19 | NO
173 | PNMT | PNMT | PNMT | 13776 | -0.068 | 0.19 | NO
174 | PSMD13 | PSMD13 | PSMD13 | 14082 | -0.074 | 0.17 | NO
175 | PSMB10 | PSMB10 | PSMB10 | 14346 | -0.08 | 0.16 | NO
176 | SLC6A8 | SLC6A8 | SLC6A8 | 14428 | -0.082 | 0.16 | NO
177 | SMOX | SMOX | SMOX | 14687 | -0.089 | 0.14 | NO
178 | APIP | APIP | APIP | 14703 | -0.089 | 0.14 | NO
179 | PCSK1 | PCSK1 | PCSK1 | 14802 | -0.092 | 0.14 | NO
180 | LHB | LHB | LHB | 15223 | -0.1 | 0.12 | NO
181 | BCAT2 | BCAT2 | BCAT2 | 15459 | -0.11 | 0.11 | NO
182 | IDO1 | IDO1 | IDO1 | 15577 | -0.12 | 0.1 | NO
183 | MRI1 | MRI1 | MRI1 | 15757 | -0.12 | 0.097 | NO
184 | BCAT1 | BCAT1 | BCAT1 | 15968 | -0.13 | 0.088 | NO
185 | CCBL2 | CCBL2 | CCBL2 | 16060 | -0.14 | 0.085 | NO
186 | CGB8 | CGB8 | CGB8 | 16406 | -0.16 | 0.069 | NO
187 | CKMT1A | CKMT1A | CKMT1A | 16620 | -0.17 | 0.061 | NO
188 | CKMT1B | CKMT1B | CKMT1B | 16739 | -0.18 | 0.058 | NO
189 | CGB | CGB | CGB | 16864 | -0.19 | 0.055 | NO
190 | CGB5 | CGB5 | CGB5 | 16933 | -0.2 | 0.055 | NO
191 | ADC | ADC | ADC | 17351 | -0.25 | 0.036 | NO
192 | TPO | TPO | TPO | 17742 | -0.32 | 0.021 | NO

Figure S87. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS.

Figure S88. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM

Table S45. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | GYS2 | GYS2 | GYS2 | 4 | 2.8 | 0.21 | YES
2 | PFKFB1 | PFKFB1 | PFKFB1 | 89 | 1.5 | 0.32 | YES
3 | ALDOB | ALDOB | ALDOB | 129 | 1.2 | 0.41 | YES
4 | PCK1 | PCK1 | PCK1 | 140 | 1.2 | 0.5 | YES
5 | PKLR | PKLR | PKLR | 279 | 0.74 | 0.55 | YES
6 | PC | PC | PC | 465 | 0.5 | 0.57 | YES
7 | FBP1 | FBP1 | FBP1 | 490 | 0.48 | 0.61 | YES
8 | PYGL | PYGL | PYGL | 618 | 0.4 | 0.63 | YES
9 | PCK2 | PCK2 | PCK2 | 791 | 0.33 | 0.65 | YES
10 | PGAM2 | PGAM2 | PGAM2 | 1378 | 0.22 | 0.63 | YES
11 | PPP2R1B | PPP2R1B | PPP2R1B | 1464 | 0.21 | 0.64 | YES
12 | GOT1 | GOT1 | GOT1 | 1532 | 0.2 | 0.65 | YES
13 | SLC25A13 | SLC25A13 | SLC25A13 | 1706 | 0.18 | 0.66 | YES
14 | SLC25A10 | SLC25A10 | SLC25A10 | 1832 | 0.17 | 0.66 | YES
15 | GOT2 | GOT2 | GOT2 | 1968 | 0.16 | 0.67 | YES
16 | PGM1 | PGM1 | PGM1 | 2116 | 0.15 | 0.67 | YES
17 | UGP2 | UGP2 | UGP2 | 2161 | 0.15 | 0.68 | YES
18 | ENO3 | ENO3 | ENO3 | 2164 | 0.15 | 0.69 | YES
19 | SLC25A12 | SLC25A12 | SLC25A12 | 2866 | 0.11 | 0.66 | NO
20 | AGL | AGL | AGL | 2966 | 0.11 | 0.66 | NO
21 | GBE1 | GBE1 | GBE1 | 3212 | 0.1 | 0.66 | NO
22 | PRKACB | PRKACB | PRKACB | 3272 | 0.097 | 0.66 | NO
23 | ALDOC | ALDOC | ALDOC | 3400 | 0.094 | 0.66 | NO
24 | MDH1 | MDH1 | MDH1 | 3617 | 0.088 | 0.66 | NO
25 | PHKA2 | PHKA2 | PHKA2 | 4059 | 0.075 | 0.64 | NO
26 | GAPDHS | GAPDHS | GAPDHS | 4161 | 0.073 | 0.64 | NO
27 | PFKFB3 | PFKFB3 | PFKFB3 | 4816 | 0.057 | 0.61 | NO
28 | PRKACA | PRKACA | PRKACA | 5473 | 0.044 | 0.57 | NO
29 | MDH2 | MDH2 | MDH2 | 5897 | 0.037 | 0.55 | NO
30 | PGM2 | PGM2 | PGM2 | 6058 | 0.035 | 0.55 | NO
31 | PGAM1 | PGAM1 | PGAM1 | 6294 | 0.032 | 0.54 | NO
32 | PHKA1 | PHKA1 | PHKA1 | 6446 | 0.03 | 0.53 | NO
33 | PPP2CA | PPP2CA | PPP2CA | 6548 | 0.028 | 0.53 | NO
34 | PHKB | PHKB | PHKB | 6926 | 0.023 | 0.51 | NO
35 | GYG1 | GYG1 | GYG1 | 7237 | 0.019 | 0.49 | NO
36 | SLC25A1 | SLC25A1 | SLC25A1 | 7615 | 0.014 | 0.47 | NO
37 | PFKM | PFKM | PFKM | 7898 | 0.011 | 0.46 | NO
38 | GPI | GPI | GPI | 8060 | 0.0088 | 0.45 | NO
39 | PFKFB2 | PFKFB2 | PFKFB2 | 8089 | 0.0084 | 0.45 | NO
40 | PPP2R1A | PPP2R1A | PPP2R1A | 8321 | 0.0054 | 0.44 | NO
41 | SLC25A11 | SLC25A11 | SLC25A11 | 8355 | 0.0051 | 0.43 | NO
42 | PGK1 | PGK1 | PGK1 | 9470 | -0.0074 | 0.37 | NO
43 | ENO1 | ENO1 | ENO1 | 9872 | -0.012 | 0.35 | NO
44 | PFKL | PFKL | PFKL | 9990 | -0.013 | 0.35 | NO
45 | CALM2 | CALM2 | CALM2 | 10082 | -0.014 | 0.34 | NO
46 | PPP2CB | PPP2CB | PPP2CB | 10091 | -0.014 | 0.34 | NO
47 | GAPDH | GAPDH | GAPDH | 10701 | -0.022 | 0.31 | NO
48 | PPP2R5D | PPP2R5D | PPP2R5D | 10729 | -0.022 | 0.31 | NO
49 | TPI1 | TPI1 | TPI1 | 11099 | -0.027 | 0.29 | NO
50 | PYGM | PYGM | PYGM | 11536 | -0.033 | 0.27 | NO
51 | PHKG2 | PHKG2 | PHKG2 | 11783 | -0.036 | 0.26 | NO
52 | CALM3 | CALM3 | CALM3 | 11933 | -0.038 | 0.25 | NO
53 | CALM1 | CALM1 | CALM1 | 12264 | -0.043 | 0.24 | NO
54 | PYGB | PYGB | PYGB | 12513 | -0.046 | 0.23 | NO
55 | ALDOA | ALDOA | ALDOA | 13590 | -0.064 | 0.17 | NO
56 | GYG2 | GYG2 | GYG2 | 13961 | -0.072 | 0.16 | NO
57 | PKM2 | PKM2 | PKM2 | 15166 | -0.1 | 0.1 | NO
58 | GYS1 | GYS1 | GYS1 | 15308 | -0.11 | 0.1 | NO
59 | PFKP | PFKP | PFKP | 15414 | -0.11 | 0.1 | NO
60 | PHKG1 | PHKG1 | PHKG1 | 16735 | -0.18 | 0.044 | NO
61 | ENO2 | ENO2 | ENO2 | 16948 | -0.2 | 0.048 | NO
62 | PFKFB4 | PFKFB4 | PFKFB4 | 17143 | -0.22 | 0.054 | NO

Figure S89. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM.

Figure S90. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG FATTY ACID METABOLISM

Table S46. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | TAT | TAT | TAT | 27 | 1.9 | 0.17 | YES
2 | BHMT | BHMT | BHMT | 60 | 1.7 | 0.31 | YES
3 | CDO1 | CDO1 | CDO1 | 67 | 1.6 | 0.45 | YES
4 | DNMT3L | DNMT3L | DNMT3L | 131 | 1.2 | 0.56 | YES
5 | MAT1A | MAT1A | MAT1A | 190 | 1 | 0.64 | YES
6 | SDS | SDS | SDS | 284 | 0.73 | 0.7 | YES
7 | CTH | CTH | CTH | 318 | 0.67 | 0.76 | YES
8 | CBS | CBS | CBS | 739 | 0.34 | 0.76 | YES
9 | LDHAL6B | LDHAL6B | LDHAL6B | 795 | 0.33 | 0.79 | YES
10 | LDHC | LDHC | LDHC | 1468 | 0.21 | 0.77 | NO
11 | GOT1 | GOT1 | GOT1 | 1532 | 0.2 | 0.78 | NO
12 | GOT2 | GOT2 | GOT2 | 1968 | 0.16 | 0.77 | NO
13 | LDHAL6A | LDHAL6A | LDHAL6A | 2287 | 0.14 | 0.77 | NO
14 | MPST | MPST | MPST | 3093 | 0.1 | 0.73 | NO
15 | ADI1 | ADI1 | ADI1 | 3269 | 0.098 | 0.73 | NO
16 | AHCY | AHCY | AHCY | 4629 | 0.062 | 0.66 | NO
17 | MAT2A | MAT2A | MAT2A | 5257 | 0.049 | 0.63 | NO
18 | MTAP | MTAP | MTAP | 5801 | 0.038 | 0.61 | NO
19 | AHCYL1 | AHCYL1 | AHCYL1 | 5893 | 0.037 | 0.6 | NO
20 | MTR | MTR | MTR | 7532 | 0.015 | 0.52 | NO
21 | MAT2B | MAT2B | MAT2B | 7683 | 0.013 | 0.51 | NO
22 | DNMT1 | DNMT1 | DNMT1 | 8359 | 0.005 | 0.47 | NO
23 | AHCYL2 | AHCYL2 | AHCYL2 | 8476 | 0.0037 | 0.46 | NO
24 | SRM | SRM | SRM | 8631 | 0.0018 | 0.46 | NO
25 | LDHA | LDHA | LDHA | 9002 | -0.0022 | 0.44 | NO
26 | AMD1 | AMD1 | AMD1 | 9570 | -0.0085 | 0.4 | NO
27 | SMS | SMS | SMS | 11054 | -0.026 | 0.32 | NO
28 | LDHB | LDHB | LDHB | 13454 | -0.062 | 0.2 | NO
29 | ENOPH1 | ENOPH1 | ENOPH1 | 13723 | -0.067 | 0.19 | NO
30 | DNMT3B | DNMT3B | DNMT3B | 14566 | -0.086 | 0.15 | NO
31 | APIP | APIP | APIP | 14703 | -0.089 | 0.15 | NO
32 | TRDMT1 | TRDMT1 | TRDMT1 | 14721 | -0.09 | 0.16 | NO
33 | DNMT3A | DNMT3A | DNMT3A | 14886 | -0.094 | 0.16 | NO
34 | IL4I1 | IL4I1 | IL4I1 | 17380 | -0.25 | 0.04 | NO

Figure S91. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG FATTY ACID METABOLISM.

Figure S92. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG FATTY ACID METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG STEROID HORMONE BIOSYNTHESIS

Table S47. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | DPYS | DPYS | DPYS | 44 | 1.8 | 0.17 | YES
2 | UPB1 | UPB1 | UPB1 | 72 | 1.6 | 0.32 | YES
3 | UPP2 | UPP2 | UPP2 | 270 | 0.78 | 0.38 | YES
4 | DPYD | DPYD | DPYD | 844 | 0.32 | 0.38 | YES
5 | DHODH | DHODH | DHODH | 866 | 0.31 | 0.41 | YES
6 | POLR3G | POLR3G | POLR3G | 900 | 0.3 | 0.43 | YES
7 | CDA | CDA | CDA | 918 | 0.3 | 0.46 | YES
8 | ENTPD5 | ENTPD5 | ENTPD5 | 968 | 0.29 | 0.48 | YES
9 | POLE2 | POLE2 | POLE2 | 1239 | 0.24 | 0.49 | YES
10 | RRM2 | RRM2 | RRM2 | 1650 | 0.19 | 0.49 | NO
11 | NT5C1B | NT5C1B | NT5C1B | 2090 | 0.16 | 0.48 | NO
12 | ENTPD8 | ENTPD8 | ENTPD8 | 2433 | 0.14 | 0.47 | NO
13 | NT5E | NT5E | NT5E | 2540 | 0.13 | 0.48 | NO
14 | TK1 | TK1 | TK1 | 3001 | 0.11 | 0.46 | NO
15 | NME1-NME2 | NME1-NME2 | NME1-NME2 | 3845 | 0.081 | 0.42 | NO
16 | TYMS | TYMS | TYMS | 4068 | 0.075 | 0.42 | NO
17 | CMPK1 | CMPK1 | CMPK1 | 4399 | 0.067 | 0.41 | NO
18 | PNP | PNP | PNP | 4901 | 0.055 | 0.38 | NO
19 | POLR3A | POLR3A | POLR3A | 4978 | 0.054 | 0.38 | NO
20 | POLR2C | POLR2C | POLR2C | 5361 | 0.047 | 0.37 | NO
21 | NME1 | NME1 | NME1 | 5373 | 0.046 | 0.37 | NO
22 | NT5M | NT5M | NT5M | 5380 | 0.046 | 0.38 | NO
23 | TXNRD2 | TXNRD2 | TXNRD2 | 5436 | 0.045 | 0.38 | NO
24 | AK3 | AK3 | AK3 | 5598 | 0.042 | 0.37 | NO
25 | POLD4 | POLD4 | POLD4 | 5683 | 0.04 | 0.37 | NO
26 | UPRT | UPRT | UPRT | 5916 | 0.037 | 0.36 | NO
27 | POLR2F | POLR2F | POLR2F | 5941 | 0.036 | 0.36 | NO
28 | POLD2 | POLD2 | POLD2 | 5954 | 0.036 | 0.37 | NO
29 | NME4 | NME4 | NME4 | 6064 | 0.035 | 0.36 | NO
30 | NUDT2 | NUDT2 | NUDT2 | 6556 | 0.028 | 0.34 | NO
31 | POLR1B | POLR1B | POLR1B | 6709 | 0.026 | 0.33 | NO
32 | NT5C2 | NT5C2 | NT5C2 | 6956 | 0.023 | 0.32 | NO
33 | CAD | CAD | CAD | 7404 | 0.017 | 0.3 | NO
34 | PNPT1 | PNPT1 | PNPT1 | 7547 | 0.015 | 0.29 | NO
35 | POLE | POLE | POLE | 7602 | 0.014 | 0.29 | NO
36 | POLR1A | POLR1A | POLR1A | 7830 | 0.011 | 0.28 | NO
37 | NME2 | NME2 | NME2 | 7935 | 0.01 | 0.28 | NO
38 | POLR3H | POLR3H | POLR3H | 7955 | 0.01 | 0.28 | NO
39 | POLR2E | POLR2E | POLR2E | 8034 | 0.009 | 0.27 | NO
40 | TYMP | TYMP | TYMP | 8112 | 0.0082 | 0.27 | NO
41 | POLE4 | POLE4 | POLE4 | 8495 | 0.0035 | 0.25 | NO
42 | POLR3B | POLR3B | POLR3B | 8543 | 0.0029 | 0.24 | NO
43 | CANT1 | CANT1 | CANT1 | 8554 | 0.0028 | 0.24 | NO
44 | UPP1 | UPP1 | UPP1 | 8705 | 0.0011 | 0.24 | NO
45 | RRM2B | RRM2B | RRM2B | 8994 | -0.0021 | 0.22 | NO
46 | POLR2G | POLR2G | POLR2G | 9127 | -0.0035 | 0.21 | NO
47 | TK2 | TK2 | TK2 | 9179 | -0.0042 | 0.21 | NO
48 | POLR2D | POLR2D | POLR2D | 9584 | -0.0087 | 0.19 | NO
49 | POLR1E | POLR1E | POLR1E | 9690 | -0.01 | 0.18 | NO
50 | POLD1 | POLD1 | POLD1 | 9777 | -0.011 | 0.18 | NO
51 | POLE3 | POLE3 | POLE3 | 9811 | -0.011 | 0.18 | NO
52 | UCK1 | UCK1 | UCK1 | 10073 | -0.014 | 0.17 | NO
53 | UMPS | UMPS | UMPS | 10236 | -0.016 | 0.16 | NO
54 | POLR2J | POLR2J | POLR2J | 10264 | -0.017 | 0.16 | NO
55 | POLR3GL | POLR3GL | POLR3GL | 10516 | -0.02 | 0.15 | NO
56 | POLR2H | POLR2H | POLR2H | 10531 | -0.02 | 0.15 | NO
57 | POLR3F | POLR3F | POLR3F | 10582 | -0.02 | 0.15 | NO
58 | DTYMK | DTYMK | DTYMK | 10618 | -0.021 | 0.15 | NO
59 | POLR2I | POLR2I | POLR2I | 10880 | -0.024 | 0.14 | NO
60 | POLR2K | POLR2K | POLR2K | 11010 | -0.026 | 0.13 | NO
61 | NME5 | NME5 | NME5 | 11013 | -0.026 | 0.13 | NO
62 | TXNRD1 | TXNRD1 | TXNRD1 | 11066 | -0.026 | 0.13 | NO
63 | ENTPD6 | ENTPD6 | ENTPD6 | 11513 | -0.032 | 0.11 | NO
64 | RRM1 | RRM1 | RRM1 | 11628 | -0.034 | 0.11 | NO
65 | CMPK2 | CMPK2 | CMPK2 | 11748 | -0.036 | 0.1 | NO
66 | POLR3K | POLR3K | POLR3K | 12141 | -0.041 | 0.087 | NO
67 | POLD3 | POLD3 | POLD3 | 12143 | -0.041 | 0.091 | NO
68 | POLA2 | POLA2 | POLA2 | 12452 | -0.046 | 0.078 | NO
69 | NT5C3 | NT5C3 | NT5C3 | 12592 | -0.048 | 0.075 | NO
70 | ENTPD3 | ENTPD3 | ENTPD3 | 12887 | -0.053 | 0.064 | NO
71 | PRIM1 | PRIM1 | PRIM1 | 13176 | -0.057 | 0.053 | NO
72 | POLR2A | POLR2A | POLR2A | 13308 | -0.059 | 0.052 | NO
73 | NME6 | NME6 | NME6 | 13412 | -0.061 | 0.052 | NO
74 | CTPS | CTPS | CTPS | 13600 | -0.064 | 0.047 | NO
75 | POLR3C | POLR3C | POLR3C | 13655 | -0.065 | 0.051 | NO
76 | DUT | DUT | DUT | 13700 | -0.066 | 0.054 | NO
77 | POLR2J3 | POLR2J3 | POLR2J3 | 13780 | -0.068 | 0.057 | NO
78 | POLR2L | POLR2L | POLR2L | 14034 | -0.073 | 0.05 | NO
79 | ENTPD1 | ENTPD1 | ENTPD1 | 14134 | -0.075 | 0.051 | NO
80 | ITPA | ITPA | ITPA | 14266 | -0.078 | 0.051 | NO
81 | POLR2B | POLR2B | POLR2B | 14339 | -0.08 | 0.055 | NO
82 | ENTPD4 | ENTPD4 | ENTPD4 | 14385 | -0.081 | 0.06 | NO
83 | DCTD | DCTD | DCTD | 14520 | -0.084 | 0.061 | NO
84 | PRIM2 | PRIM2 | PRIM2 | 14579 | -0.086 | 0.066 | NO
85 | POLA1 | POLA1 | POLA1 | 14582 | -0.086 | 0.074 | NO
86 | POLR1C | POLR1C | POLR1C | 14605 | -0.087 | 0.081 | NO
87 | CTPS2 | CTPS2 | CTPS2 | 14695 | -0.089 | 0.084 | NO
88 | NT5C | NT5C | NT5C | 14741 | -0.09 | 0.091 | NO
89 | NME3 | NME3 | NME3 | 14925 | -0.096 | 0.09 | NO
90 | UCK2 | UCK2 | UCK2 | 15022 | -0.098 | 0.094 | NO
91 | NME7 | NME7 | NME7 | 15079 | -0.1 | 0.1 | NO
92 | POLR1D | POLR1D | POLR1D | 15115 | -0.1 | 0.11 | NO
93 | POLR3D | POLR3D | POLR3D | 15209 | -0.1 | 0.11 | NO
94 | ZNRD1 | ZNRD1 | ZNRD1 | 15264 | -0.11 | 0.12 | NO
95 | DCK | DCK | DCK | 15419 | -0.11 | 0.12 | NO
96 | UCKL1 | UCKL1 | UCKL1 | 15746 | -0.12 | 0.12 | NO
97 | POLR2J2 | POLR2J2 | POLR2J2 | 16583 | -0.17 | 0.085 | NO

Figure S93. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG STEROID HORMONE BIOSYNTHESIS.

Figure S94. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG STEROID HORMONE BIOSYNTHESIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PURINE METABOLISM

Table S48. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | DPYS | DPYS | DPYS | 44 | 1.8 | 0.16 | YES
2 | UPB1 | UPB1 | UPB1 | 72 | 1.6 | 0.3 | YES
3 | AGXT2 | AGXT2 | AGXT2 | 170 | 1.1 | 0.4 | YES
4 | UPP2 | UPP2 | UPP2 | 270 | 0.78 | 0.46 | YES
5 | XDH | XDH | XDH | 630 | 0.39 | 0.48 | YES
6 | DPYD | DPYD | DPYD | 844 | 0.32 | 0.5 | YES
7 | DHODH | DHODH | DHODH | 866 | 0.31 | 0.52 | YES
8 | CDA | CDA | CDA | 918 | 0.3 | 0.55 | YES
9 | GLRX | GLRX | GLRX | 976 | 0.28 | 0.57 | YES
10 | GDA | GDA | GDA | 1208 | 0.24 | 0.58 | YES
11 | AK5 | AK5 | AK5 | 1551 | 0.2 | 0.58 | YES
12 | ADSSL1 | ADSSL1 | ADSSL1 | 1639 | 0.19 | 0.6 | YES
13 | RRM2 | RRM2 | RRM2 | 1650 | 0.19 | 0.61 | YES
14 | GMPR | GMPR | GMPR | 1739 | 0.18 | 0.62 | YES
15 | CAT | CAT | CAT | 1814 | 0.18 | 0.64 | YES
16 | ADK | ADK | ADK | 2085 | 0.16 | 0.64 | YES
17 | NT5C1B | NT5C1B | NT5C1B | 2090 | 0.16 | 0.65 | YES
18 | NT5E | NT5E | NT5E | 2540 | 0.13 | 0.64 | NO
19 | ADA | ADA | ADA | 2583 | 0.13 | 0.64 | NO
20 | TK1 | TK1 | TK1 | 3001 | 0.11 | 0.63 | NO
21 | NME1-NME2 | NME1-NME2 | NME1-NME2 | 3845 | 0.081 | 0.59 | NO
22 | TYMS | TYMS | TYMS | 4068 | 0.075 | 0.59 | NO
23 | ADAL | ADAL | ADAL | 4116 | 0.074 | 0.59 | NO
24 | CMPK1 | CMPK1 | CMPK1 | 4399 | 0.067 | 0.58 | NO
25 | ADSS | ADSS | ADSS | 4791 | 0.058 | 0.57 | NO
26 | PNP | PNP | PNP | 4901 | 0.055 | 0.56 | NO
27 | GMPS | GMPS | GMPS | 5266 | 0.049 | 0.55 | NO
28 | NME1 | NME1 | NME1 | 5373 | 0.046 | 0.55 | NO
29 | NT5M | NT5M | NT5M | 5380 | 0.046 | 0.55 | NO
30 | APRT | APRT | APRT | 5411 | 0.046 | 0.55 | NO
31 | GMPR2 | GMPR2 | GMPR2 | 5625 | 0.042 | 0.55 | NO
32 | ADSL | ADSL | ADSL | 5753 | 0.039 | 0.54 | NO
33 | GUK1 | GUK1 | GUK1 | 5803 | 0.038 | 0.54 | NO
34 | NME4 | NME4 | NME4 | 6064 | 0.035 | 0.53 | NO
35 | GART | GART | GART | 6134 | 0.034 | 0.53 | NO
36 | NT5C2 | NT5C2 | NT5C2 | 6956 | 0.023 | 0.49 | NO
37 | HPRT1 | HPRT1 | HPRT1 | 7109 | 0.021 | 0.48 | NO
38 | CAD | CAD | CAD | 7404 | 0.017 | 0.47 | NO
39 | AMPD2 | AMPD2 | AMPD2 | 7745 | 0.012 | 0.45 | NO
40 | NME2 | NME2 | NME2 | 7935 | 0.01 | 0.44 | NO
41 | TYMP | TYMP | TYMP | 8112 | 0.0082 | 0.43 | NO
42 | ATIC | ATIC | ATIC | 8201 | 0.007 | 0.43 | NO
43 | AK2 | AK2 | AK2 | 8288 | 0.006 | 0.42 | NO
44 | IMPDH1 | IMPDH1 | IMPDH1 | 8315 | 0.0055 | 0.42 | NO
45 | PAICS | PAICS | PAICS | 8357 | 0.005 | 0.42 | NO
46 | UPP1 | UPP1 | UPP1 | 8705 | 0.0011 | 0.4 | NO
47 | RRM2B | RRM2B | RRM2B | 8994 | -0.0021 | 0.38 | NO
48 | TK2 | TK2 | TK2 | 9179 | -0.0042 | 0.38 | NO
49 | GPX1 | GPX1 | GPX1 | 9226 | -0.0048 | 0.37 | NO
50 | UCK1 | UCK1 | UCK1 | 10073 | -0.014 | 0.33 | NO
51 | GSR | GSR | GSR | 10199 | -0.016 | 0.32 | NO
52 | UMPS | UMPS | UMPS | 10236 | -0.016 | 0.32 | NO
53 | DTYMK | DTYMK | DTYMK | 10618 | -0.021 | 0.3 | NO
54 | PFAS | PFAS | PFAS | 10920 | -0.024 | 0.29 | NO
55 | TXNRD1 | TXNRD1 | TXNRD1 | 11066 | -0.026 | 0.28 | NO
56 | RRM1 | RRM1 | RRM1 | 11628 | -0.034 | 0.25 | NO
57 | PPAT | PPAT | PPAT | 11887 | -0.037 | 0.24 | NO
58 | DGUOK | DGUOK | DGUOK | 12084 | -0.04 | 0.24 | NO
59 | TXN | TXN | TXN | 12326 | -0.044 | 0.23 | NO
60 | NT5C3 | NT5C3 | NT5C3 | 12592 | -0.048 | 0.22 | NO
61 | AK1 | AK1 | AK1 | 13107 | -0.056 | 0.19 | NO
62 | CTPS | CTPS | CTPS | 13600 | -0.064 | 0.17 | NO
63 | DUT | DUT | DUT | 13700 | -0.066 | 0.17 | NO
64 | IMPDH2 | IMPDH2 | IMPDH2 | 14060 | -0.074 | 0.16 | NO
65 | AMPD3 | AMPD3 | AMPD3 | 14292 | -0.079 | 0.15 | NO
66 | DCTD | DCTD | DCTD | 14520 | -0.084 | 0.15 | NO
67 | CTPS2 | CTPS2 | CTPS2 | 14695 | -0.089 | 0.15 | NO
68 | NT5C | NT5C | NT5C | 14741 | -0.09 | 0.15 | NO
69 | UCK2 | UCK2 | UCK2 | 15022 | -0.098 | 0.15 | NO
70 | DCK | DCK | DCK | 15419 | -0.11 | 0.14 | NO
71 | AMPD1 | AMPD1 | AMPD1 | 16373 | -0.16 | 0.096 | NO

Figure S95. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PURINE METABOLISM.

Figure S96. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PURINE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PYRIMIDINE METABOLISM

Table S49. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | ADH4 | ADH4 | ADH4 | 43 | 1.8 | 0.12 | YES
2 | ALDOB | ALDOB | ALDOB | 129 | 1.2 | 0.2 | YES
3 | PCK1 | PCK1 | PCK1 | 140 | 1.2 | 0.28 | YES
4 | ADH1A | ADH1A | ADH1A | 147 | 1.2 | 0.36 | YES
5 | ADH1B | ADH1B | ADH1B | 196 | 0.99 | 0.43 | YES
6 | PKLR | PKLR | PKLR | 279 | 0.74 | 0.47 | YES
7 | G6PC | G6PC | G6PC | 297 | 0.69 | 0.52 | YES
8 | ADH1C | ADH1C | ADH1C | 302 | 0.69 | 0.57 | YES
9 | ADH6 | ADH6 | ADH6 | 329 | 0.66 | 0.61 | YES
10 | FBP1 | FBP1 | FBP1 | 490 | 0.48 | 0.63 | YES
11 | PCK2 | PCK2 | PCK2 | 791 | 0.33 | 0.64 | YES
12 | LDHAL6B | LDHAL6B | LDHAL6B | 795 | 0.33 | 0.66 | YES
13 | ALDH2 | ALDH2 | ALDH2 | 1082 | 0.26 | 0.66 | YES
14 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 1370 | 0.22 | 0.66 | YES
15 | PGAM2 | PGAM2 | PGAM2 | 1378 | 0.22 | 0.68 | YES
16 | LDHC | LDHC | LDHC | 1468 | 0.21 | 0.69 | YES
17 | HK3 | HK3 | HK3 | 1599 | 0.19 | 0.69 | YES
18 | ALDH1A3 | ALDH1A3 | ALDH1A3 | 1708 | 0.18 | 0.7 | YES
19 | PGM1 | PGM1 | PGM1 | 2116 | 0.15 | 0.69 | NO
20 | ENO3 | ENO3 | ENO3 | 2164 | 0.15 | 0.7 | NO
21 | LDHAL6A | LDHAL6A | LDHAL6A | 2287 | 0.14 | 0.7 | NO
22 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 2555 | 0.13 | 0.69 | NO
23 | PGAM4 | PGAM4 | PGAM4 | 2702 | 0.12 | 0.69 | NO
24 | ALDH3A1 | ALDH3A1 | ALDH3A1 | 2979 | 0.11 | 0.68 | NO
25 | GALM | GALM | GALM | 3147 | 0.1 | 0.68 | NO
26 | ALDOC | ALDOC | ALDOC | 3400 | 0.094 | 0.68 | NO
27 | PDHB | PDHB | PDHB | 4464 | 0.065 | 0.62 | NO
28 | AKR1A1 | AKR1A1 | AKR1A1 | 4495 | 0.064 | 0.62 | NO
29 | DLD | DLD | DLD | 4899 | 0.056 | 0.6 | NO
30 | PGM2 | PGM2 | PGM2 | 6058 | 0.035 | 0.54 | NO
31 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 6217 | 0.033 | 0.54 | NO
32 | PGAM1 | PGAM1 | PGAM1 | 6294 | 0.032 | 0.54 | NO
33 | PDHA1 | PDHA1 | PDHA1 | 6509 | 0.029 | 0.52 | NO
34 | ACSS2 | ACSS2 | ACSS2 | 7075 | 0.021 | 0.5 | NO
35 | PFKM | PFKM | PFKM | 7898 | 0.011 | 0.45 | NO
36 | GPI | GPI | GPI | 8060 | 0.0088 | 0.44 | NO
37 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 8254 | 0.0064 | 0.43 | NO
38 | LDHA | LDHA | LDHA | 9002 | -0.0022 | 0.39 | NO
39 | ALDH3B1 | ALDH3B1 | ALDH3B1 | 9412 | -0.0067 | 0.37 | NO
40 | PGK1 | PGK1 | PGK1 | 9470 | -0.0074 | 0.37 | NO
41 | ENO1 | ENO1 | ENO1 | 9872 | -0.012 | 0.34 | NO
42 | PFKL | PFKL | PFKL | 9990 | -0.013 | 0.34 | NO
43 | ADH5 | ADH5 | ADH5 | 10368 | -0.018 | 0.32 | NO
44 | BPGM | BPGM | BPGM | 10665 | -0.021 | 0.3 | NO
45 | GAPDH | GAPDH | GAPDH | 10701 | -0.022 | 0.3 | NO
46 | ACSS1 | ACSS1 | ACSS1 | 11074 | -0.027 | 0.28 | NO
47 | TPI1 | TPI1 | TPI1 | 11099 | -0.027 | 0.28 | NO
48 | DLAT | DLAT | DLAT | 12129 | -0.041 | 0.23 | NO
49 | HK2 | HK2 | HK2 | 12234 | -0.042 | 0.23 | NO
50 | HK1 | HK1 | HK1 | 13126 | -0.056 | 0.18 | NO
51 | LDHB | LDHB | LDHB | 13454 | -0.062 | 0.17 | NO
52 | ALDOA | ALDOA | ALDOA | 13590 | -0.064 | 0.17 | NO
53 | PKM2 | PKM2 | PKM2 | 15166 | -0.1 | 0.086 | NO
54 | PFKP | PFKP | PFKP | 15414 | -0.11 | 0.08 | NO
55 | GCK | GCK | GCK | 16688 | -0.18 | 0.022 | NO
56 | ENO2 | ENO2 | ENO2 | 16948 | -0.2 | 0.021 | NO
57 | ALDH3B2 | ALDH3B2 | ALDH3B2 | 17479 | -0.27 | 0.01 | NO
58 | G6PC2 | G6PC2 | G6PC2 | 17869 | -0.36 | 0.014 | NO

Figure S97. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PYRIMIDINE METABOLISM.

Figure S98. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PYRIMIDINE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM

Table S50. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | CYP8B1 | CYP8B1 | CYP8B1 | 28 | 1.9 | 0.071 | YES
2 | APOA5 | APOA5 | APOA5 | 29 | 1.9 | 0.14 | YES
3 | CYP4A22 | CYP4A22 | CYP4A22 | 31 | 1.9 | 0.22 | YES
4 | APOC3 | APOC3 | APOC3 | 61 | 1.7 | 0.28 | YES
5 | APOA1 | APOA1 | APOA1 | 83 | 1.5 | 0.33 | YES
6 | FABP1 | FABP1 | FABP1 | 121 | 1.3 | 0.38 | YES
7 | PCK1 | PCK1 | PCK1 | 140 | 1.2 | 0.42 | YES
8 | CYP7A1 | CYP7A1 | CYP7A1 | 144 | 1.2 | 0.47 | YES
9 | APOA2 | APOA2 | APOA2 | 155 | 1.1 | 0.51 | YES
10 | SLC27A5 | SLC27A5 | SLC27A5 | 156 | 1.1 | 0.55 | YES
11 | HMGCS2 | HMGCS2 | HMGCS2 | 175 | 1 | 0.59 | YES
12 | ACOX2 | ACOX2 | ACOX2 | 226 | 0.87 | 0.62 | YES
13 | CYP4A11 | CYP4A11 | CYP4A11 | 239 | 0.83 | 0.65 | YES
14 | PLIN1 | PLIN1 | PLIN1 | 242 | 0.83 | 0.68 | YES
15 | ACADL | ACADL | ACADL | 288 | 0.72 | 0.71 | YES
16 | EHHADH | EHHADH | EHHADH | 333 | 0.65 | 0.73 | YES
17 | ACSL1 | ACSL1 | ACSL1 | 473 | 0.49 | 0.74 | YES
18 | SLC27A2 | SLC27A2 | SLC27A2 | 507 | 0.46 | 0.76 | YES
19 | CYP27A1 | CYP27A1 | CYP27A1 | 581 | 0.42 | 0.77 | YES
20 | CD36 | CD36 | CD36 | 651 | 0.38 | 0.78 | YES
21 | PCK2 | PCK2 | PCK2 | 791 | 0.33 | 0.78 | YES
22 | ANGPTL4 | ANGPTL4 | ANGPTL4 | 805 | 0.33 | 0.79 | YES
23 | ACSL6 | ACSL6 | ACSL6 | 864 | 0.31 | 0.8 | YES
24 | FABP3 | FABP3 | FABP3 | 1179 | 0.25 | 0.79 | YES
25 | ACSL5 | ACSL5 | ACSL5 | 1246 | 0.24 | 0.8 | YES
26 | SCD | SCD | SCD | 1387 | 0.22 | 0.8 | YES
27 | FABP4 | FABP4 | FABP4 | 1465 | 0.21 | 0.8 | YES
28 | ACAA1 | ACAA1 | ACAA1 | 1754 | 0.18 | 0.8 | YES
29 | SCP2 | SCP2 | SCP2 | 1818 | 0.18 | 0.8 | YES
30 | ACADM | ACADM | ACADM | 1865 | 0.17 | 0.8 | YES
31 | RXRG | RXRG | RXRG | 1917 | 0.17 | 0.8 | YES
32 | CPT2 | CPT2 | CPT2 | 1964 | 0.16 | 0.81 | YES
33 | PPARA | PPARA | PPARA | 1990 | 0.16 | 0.81 | YES
34 | ACOX1 | ACOX1 | ACOX1 | 2024 | 0.16 | 0.82 | YES
35 | SORBS1 | SORBS1 | SORBS1 | 2470 | 0.13 | 0.8 | NO
36 | CPT1C | CPT1C | CPT1C | 2480 | 0.13 | 0.8 | NO
37 | AQP7 | AQP7 | AQP7 | 3697 | 0.085 | 0.74 | NO
38 | ACSL3 | ACSL3 | ACSL3 | 4014 | 0.076 | 0.72 | NO
39 | GK | GK | GK | 5111 | 0.052 | 0.66 | NO
40 | CPT1A | CPT1A | CPT1A | 5540 | 0.043 | 0.64 | NO
41 | ME1 | ME1 | ME1 | 6698 | 0.026 | 0.58 | NO
42 | RXRA | RXRA | RXRA | 7058 | 0.021 | 0.56 | NO
43 | FABP5 | FABP5 | FABP5 | 7106 | 0.021 | 0.56 | NO
44 | PDPK1 | PDPK1 | PDPK1 | 7420 | 0.016 | 0.54 | NO
45 | PLTP | PLTP | PLTP | 7779 | 0.012 | 0.52 | NO
46 | ACOX3 | ACOX3 | ACOX3 | 7887 | 0.011 | 0.52 | NO
47 | PPARG | PPARG | PPARG | 8013 | 0.0092 | 0.51 | NO
48 | CPT1B | CPT1B | CPT1B | 8122 | 0.0081 | 0.5 | NO
49 | SLC27A4 | SLC27A4 | SLC27A4 | 9019 | -0.0025 | 0.46 | NO
50 | PPARD | PPARD | PPARD | 9334 | -0.0059 | 0.44 | NO
51 | UBC | UBC | UBC | 9593 | -0.0088 | 0.42 | NO
52 | DBI | DBI | DBI | 10492 | -0.019 | 0.38 | NO
53 | RXRB | RXRB | RXRB | 10934 | -0.025 | 0.35 | NO
54 | FADS2 | FADS2 | FADS2 | 10935 | -0.025 | 0.35 | NO
55 | FABP6 | FABP6 | FABP6 | 11291 | -0.03 | 0.33 | NO
56 | SLC27A1 | SLC27A1 | SLC27A1 | 12327 | -0.044 | 0.28 | NO
57 | ILK | ILK | ILK | 12767 | -0.051 | 0.26 | NO
58 | NR1H3 | NR1H3 | NR1H3 | 13296 | -0.059 | 0.23 | NO
59 | ACSL4 | ACSL4 | ACSL4 | 13367 | -0.06 | 0.23 | NO
60 | SCD5 | SCD5 | SCD5 | 14093 | -0.074 | 0.19 | NO
61 | OLR1 | OLR1 | OLR1 | 15569 | -0.12 | 0.11 | NO
62 | LPL | LPL | LPL | 15982 | -0.13 | 0.095 | NO
63 | MMP1 | MMP1 | MMP1 | 17642 | -0.3 | 0.014 | NO
64 | SLC27A6 | SLC27A6 | SLC27A6 | 17735 | -0.32 | 0.021 | NO

Figure S99. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM.

Figure S100. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

For the top enriched genes, if you want to check whether they are

- up-regulated, please check the list of up-regulated genes

- down-regulated, please check the list of down-regulated genes

Expression level

For the top enriched genes, if you want to check whether they are

- highly expressed genes, please check the list of high (top 30%) expressed genes

- low expressed genes, please check the list of low (bottom 30%) expressed genes

An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap

Significant gene list

For the top enriched genes, if you want to check whether they are

- significantly differently expressed genes by eBayes lm fit, please check the list of significant genes

Subtype clus6 enriched pathways

Table 8. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus6. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
KEGG NOTCH SIGNALING PATHWAY | 47 | genes.ES.table | 0.35 | 1.3 | 0.15 | 1 | 1 | 0.3 | 0.2 | 0.24 | 1 | 0.86
ST ERK1 ERK2 MAPK PATHWAY | 31 | genes.ES.table | 0.3 | 1.2 | 0.23 | 1 | 1 | 0.48 | 0.32 | 0.33 | 1 | 0.8
PID INTEGRIN3 PATHWAY | 43 | genes.ES.table | 0.48 | 1.2 | 0.25 | 1 | 1 | 0.42 | 0.22 | 0.33 | 1 | 0.78
PID RHOA REG PATHWAY | 44 | genes.ES.table | 0.39 | 1.3 | 0.13 | 1 | 1 | 0.46 | 0.26 | 0.34 | 1 | 0.88
PID NECTIN PATHWAY | 30 | genes.ES.table | 0.39 | 1.2 | 0.28 | 1 | 1 | 0.3 | 0.24 | 0.23 | 1 | 0.83
PID TGFBRPATHWAY | 55 | genes.ES.table | 0.43 | 1.7 | 0.032 | 1 | 0.84 | 0.27 | 0.23 | 0.21 | 1 | 0.64
REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS | 38 | genes.ES.table | 0.38 | 1.3 | 0.12 | 1 | 1 | 0.37 | 0.27 | 0.27 | 1 | 0.87
REACTOME PRE NOTCH TRANSCRIPTION AND TRANSLATION | 27 | genes.ES.table | 0.47 | 1.5 | 0.098 | 1 | 0.98 | 0.74 | 0.38 | 0.46 | 1 | 0.72
REACTOME PRE NOTCH EXPRESSION AND PROCESSING | 41 | genes.ES.table | 0.31 | 1.2 | 0.21 | 1 | 1 | 0.42 | 0.33 | 0.28 | 1 | 0.81
REACTOME NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION | 44 | genes.ES.table | 0.43 | 1.6 | 0.061 | 1 | 0.96 | 0.43 | 0.33 | 0.29 | 1 | 0.63

genes ES table in pathway: KEGG NOTCH SIGNALING PATHWAY

Table S51. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | DACT2 | DACT2 | DACT2 | 99 | 0.64 | 0.11 | YES
2 | CTGF | CTGF | CTGF | 548 | 0.39 | 0.15 | YES
3 | BAMBI | BAMBI | BAMBI | 558 | 0.39 | 0.22 | YES
4 | TGFB2 | TGFB2 | TGFB2 | 625 | 0.37 | 0.28 | YES
5 | SMAD7 | SMAD7 | SMAD7 | 1537 | 0.25 | 0.28 | YES
6 | OCLN | OCLN | OCLN | 1660 | 0.24 | 0.31 | YES
7 | TGFBRAP1 | TGFBRAP1 | TGFBRAP1 | 1697 | 0.23 | 0.35 | YES
8 | TGFBR3 | TGFBR3 | TGFBR3 | 2037 | 0.21 | 0.37 | YES
9 | ZFYVE9 | ZFYVE9 | ZFYVE9 | 2200 | 0.2 | 0.4 | YES
10 | SMURF2 | SMURF2 | SMURF2 | 2784 | 0.16 | 0.39 | YES
11 | SKIL | SKIL | SKIL | 3199 | 0.14 | 0.39 | YES
12 | PPP2R2A | PPP2R2A | PPP2R2A | 3495 | 0.13 | 0.4 | YES
13 | SHC1 | SHC1 | SHC1 | 3529 | 0.13 | 0.42 | YES
14 | PPP2CB | PPP2CB | PPP2CB | 3854 | 0.12 | 0.42 | YES
15 | WWP1 | WWP1 | WWP1 | 4134 | 0.11 | 0.43 | YES
16 | ZFYVE16 | ZFYVE16 | ZFYVE16 | 4610 | 0.091 | 0.42 | NO
17 | SMAD4 | SMAD4 | SMAD4 | 4853 | 0.084 | 0.42 | NO
18 | PDPK1 | PDPK1 | PDPK1 | 5007 | 0.08 | 0.42 | NO
19 | TAB1 | TAB1 | TAB1 | 5374 | 0.07 | 0.42 | NO
20 | XIAP | XIAP | XIAP | 6021 | 0.054 | 0.39 | NO
21 | PPP1R15A | PPP1R15A | PPP1R15A | 6264 | 0.048 | 0.38 | NO
22 | YWHAE | YWHAE | YWHAE | 6529 | 0.043 | 0.38 | NO
23 | CTNNB1 | CTNNB1 | CTNNB1 | 6607 | 0.041 | 0.38 | NO
24 | YAP1 | YAP1 | YAP1 | 6796 | 0.037 | 0.38 | NO
25 | SMAD2 | SMAD2 | SMAD2 | 7026 | 0.032 | 0.37 | NO
26 | TGFB1 | TGFB1 | TGFB1 | 7051 | 0.032 | 0.38 | NO
27 | DAXX | DAXX | DAXX | 7410 | 0.025 | 0.36 | NO
28 | TGFB3 | TGFB3 | TGFB3 | 7775 | 0.018 | 0.34 | NO
29 | AXIN1 | AXIN1 | AXIN1 | 7933 | 0.015 | 0.34 | NO
30 | FKBP1A | FKBP1A | FKBP1A | 8525 | 0.0037 | 0.3 | NO
31 | RHOA | RHOA | RHOA | 8539 | 0.0034 | 0.3 | NO
32 | RNF111 | RNF111 | RNF111 | 8583 | 0.0028 | 0.3 | NO
33 | ITCH | ITCH | ITCH | 8640 | 0.0019 | 0.3 | NO
34 | SMAD3 | SMAD3 | SMAD3 | 8685 | 0.0011 | 0.3 | NO
35 | STRAP | STRAP | STRAP | 8850 | -0.0018 | 0.29 | NO
36 | SMURF1 | SMURF1 | SMURF1 | 8971 | -0.004 | 0.28 | NO
37 | NEDD4L | NEDD4L | NEDD4L | 9041 | -0.0053 | 0.28 | NO
38 | TGFBR1 | TGFBR1 | TGFBR1 | 9571 | -0.014 | 0.25 | NO
39 | SPTBN1 | SPTBN1 | SPTBN1 | 9608 | -0.015 | 0.25 | NO
40 | DYNLRB1 | DYNLRB1 | DYNLRB1 | 10063 | -0.023 | 0.23 | NO
41 | MAP3K7 | MAP3K7 | MAP3K7 | 10225 | -0.026 | 0.23 | NO
42 | EIF2A | EIF2A | EIF2A | 10303 | -0.027 | 0.23 | NO
43 | PML | PML | PML | 11238 | -0.046 | 0.18 | NO
44 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 11443 | -0.05 | 0.18 | NO
45 | PPP2CA | PPP2CA | PPP2CA | 11653 | -0.055 | 0.18 | NO
46 | TAB2 | TAB2 | TAB2 | 11972 | -0.062 | 0.18 | NO
47 | CAV1 | CAV1 | CAV1 | 11982 | -0.062 | 0.18 | NO
48 | PPP1CA | PPP1CA | PPP1CA | 12093 | -0.065 | 0.19 | NO
49 | GRB2 | GRB2 | GRB2 | 12474 | -0.074 | 0.18 | NO
50 | TGFBR2 | TGFBR2 | TGFBR2 | 12522 | -0.076 | 0.19 | NO
51 | SOS1 | SOS1 | SOS1 | 12817 | -0.085 | 0.19 | NO
52 | DAB2 | DAB2 | DAB2 | 12986 | -0.09 | 0.2 | NO
53 | ARRB2 | ARRB2 | ARRB2 | 13205 | -0.097 | 0.2 | NO
54 | PARD6A | PARD6A | PARD6A | 13705 | -0.11 | 0.2 | NO
55 | CAMK2A | CAMK2A | CAMK2A | 15984 | -0.27 | 0.12 | NO

Figure S101. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG NOTCH SIGNALING PATHWAY.

Figure S102. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NOTCH SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: ST ERK1 ERK2 MAPK PATHWAY

Table S52. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | WWTR1 | WWTR1 | WWTR1 | 778 | 0.34 | 0.018 | YES
2 | E2F5 | E2F5 | E2F5 | 896 | 0.32 | 0.069 | YES
3 | SERPINE1 | SERPINE1 | SERPINE1 | 997 | 0.3 | 0.12 | YES
4 | PMEPA1 | PMEPA1 | PMEPA1 | 1083 | 0.3 | 0.17 | YES
5 | SMAD7 | SMAD7 | SMAD7 | 1537 | 0.25 | 0.19 | YES
6 | FURIN | FURIN | FURIN | 2148 | 0.2 | 0.19 | YES
7 | ZFYVE9 | ZFYVE9 | ZFYVE9 | 2200 | 0.2 | 0.22 | YES
8 | TGIF2 | TGIF2 | TGIF2 | 2482 | 0.18 | 0.24 | YES
9 | CGN | CGN | CGN | 2566 | 0.17 | 0.26 | YES
10 | SMURF2 | SMURF2 | SMURF2 | 2784 | 0.16 | 0.28 | YES
11 | SKIL | SKIL | SKIL | 3199 | 0.14 | 0.28 | YES
12 | F11R | F11R | F11R | 3265 | 0.14 | 0.3 | YES
13 | RBL1 | RBL1 | RBL1 | 3296 | 0.14 | 0.33 | YES
14 | SKI | SKI | SKI | 3341 | 0.14 | 0.35 | YES
15 | JUNB | JUNB | JUNB | 3534 | 0.13 | 0.36 | YES
16 | ARHGEF18 | ARHGEF18 | ARHGEF18 | 3758 | 0.12 | 0.37 | YES
17 | PARP1 | PARP1 | PARP1 | 3793 | 0.12 | 0.39 | YES
18 | CDK9 | CDK9 | CDK9 | 4209 | 0.1 | 0.39 | YES
19 | CDKN2B | CDKN2B | CDKN2B | 4391 | 0.098 | 0.39 | YES
20 | NCOR2 | NCOR2 | NCOR2 | 4640 | 0.09 | 0.4 | YES
21 | SMAD4 | SMAD4 | SMAD4 | 4853 | 0.084 | 0.4 | YES
22 | UCHL5 | UCHL5 | UCHL5 | 5062 | 0.078 | 0.4 | YES
23 | PARD3 | PARD3 | PARD3 | 5383 | 0.07 | 0.4 | YES
24 | NCOR1 | NCOR1 | NCOR1 | 5489 | 0.067 | 0.4 | YES
25 | CCNT1 | CCNT1 | CCNT1 | 5577 | 0.064 | 0.41 | YES
26 | SP1 | SP1 | SP1 | 5641 | 0.062 | 0.42 | YES
27 | PPP1R15A | PPP1R15A | PPP1R15A | 6264 | 0.048 | 0.39 | NO
28 | PPM1A | PPM1A | PPM1A | 6327 | 0.047 | 0.4 | NO
29 | TRIM33 | TRIM33 | TRIM33 | 6960 | 0.034 | 0.37 | NO
30 | SMAD2 | SMAD2 | SMAD2 | 7026 | 0.032 | 0.37 | NO
31 | TGFB1 | TGFB1 | TGFB1 | 7051 | 0.032 | 0.38 | NO
32 | UBE2D3 | UBE2D3 | UBE2D3 | 7577 | 0.022 | 0.35 | NO
33 | CCNT2 | CCNT2 | CCNT2 | 7584 | 0.022 | 0.35 | NO
34 | TGIF1 | TGIF1 | TGIF1 | 7809 | 0.017 | 0.34 | NO
35 | FKBP1A | FKBP1A | FKBP1A | 8525 | 0.0037 | 0.3 | NO
36 | RHOA | RHOA | RHOA | 8539 | 0.0034 | 0.3 | NO
37 | PPP1CC | PPP1CC | PPP1CC | 8560 | 0.0032 | 0.3 | NO
38 | USP9X | USP9X | USP9X | 8612 | 0.0025 | 0.3 | NO
39 | SMAD3 | SMAD3 | SMAD3 | 8685 | 0.0011 | 0.3 | NO
40 | STRAP | STRAP | STRAP | 8850 | -0.0018 | 0.29 | NO
41 | SMURF1 | SMURF1 | SMURF1 | 8971 | -0.004 | 0.28 | NO
42 | RPS27A | RPS27A | RPS27A | 9002 | -0.0045 | 0.28 | NO
43 | TGFBR1 | TGFBR1 | TGFBR1 | 9571 | -0.014 | 0.25 | NO
44 | UBE2D1 | UBE2D1 | UBE2D1 | 9908 | -0.02 | 0.24 | NO
45 | UBA52 | UBA52 | UBA52 | 10586 | -0.033 | 0.21 | NO
46 | MEN1 | MEN1 | MEN1 | 10711 | -0.036 | 0.21 | NO
47 | MTMR4 | MTMR4 | MTMR4 | 10901 | -0.039 | 0.2 | NO
48 | CCNC | CCNC | CCNC | 11183 | -0.045 | 0.2 | NO
49 | XPO1 | XPO1 | XPO1 | 11253 | -0.046 | 0.2 | NO
50 | STUB1 | STUB1 | STUB1 | 11656 | -0.055 | 0.19 | NO
51 | HDAC1 | HDAC1 | HDAC1 | 11744 | -0.057 | 0.19 | NO
52 | PPP1CB | PPP1CB | PPP1CB | 11770 | -0.057 | 0.2 | NO
53 | PRKCZ | PRKCZ | PRKCZ | 11991 | -0.062 | 0.2 | NO
54 | PPP1CA | PPP1CA | PPP1CA | 12093 | -0.065 | 0.21 | NO
55 | TGFBR2 | TGFBR2 | TGFBR2 | 12522 | -0.076 | 0.2 | NO
56 | TFDP1 | TFDP1 | TFDP1 | 12753 | -0.083 | 0.2 | NO
57 | MYC | MYC | MYC | 13449 | -0.1 | 0.18 | NO
58 | PARD6A | PARD6A | PARD6A | 13705 | -0.11 | 0.19 | NO
59 | CDK8 | CDK8 | CDK8 | 14027 | -0.13 | 0.19 | NO
60 | E2F4 | E2F4 | E2F4 | 15123 | -0.19 | 0.17 | NO

Figure S103. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: ST ERK1 ERK2 MAPK PATHWAY.

Figure S104. Get High-res Image For the top 5 core enriched genes in the pathway: ST ERK1 ERK2 MAPK PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID INTEGRIN3 PATHWAY

Table S53. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | TLE2 | TLE2 | TLE2 | 454 | 0.41 | 0.074 | YES
2 | HEY1 | HEY1 | HEY1 | 730 | 0.34 | 0.14 | YES
3 | MAML3 | MAML3 | MAML3 | 735 | 0.34 | 0.22 | YES
4 | MAMLD1 | MAMLD1 | MAMLD1 | 1011 | 0.3 | 0.28 | YES
5 | MAML2 | MAML2 | MAML2 | 1501 | 0.25 | 0.32 | YES
6 | HES1 | HES1 | HES1 | 1886 | 0.22 | 0.35 | YES
7 | HDAC11 | HDAC11 | HDAC11 | 2444 | 0.18 | 0.36 | YES
8 | TLE4 | TLE4 | TLE4 | 2668 | 0.17 | 0.39 | YES
9 | HDAC5 | HDAC5 | HDAC5 | 2840 | 0.16 | 0.42 | YES
10 | HDAC7 | HDAC7 | HDAC7 | 3984 | 0.11 | 0.38 | YES
11 | TLE1 | TLE1 | TLE1 | 4408 | 0.097 | 0.38 | YES
12 | NCOR2 | NCOR2 | NCOR2 | 4640 | 0.09 | 0.39 | YES
13 | MAML1 | MAML1 | MAML1 | 5273 | 0.073 | 0.37 | YES
14 | HDAC4 | HDAC4 | HDAC4 | 5359 | 0.07 | 0.38 | YES
15 | KAT2A | KAT2A | KAT2A | 5366 | 0.07 | 0.4 | YES
16 | NCOR1 | NCOR1 | NCOR1 | 5489 | 0.067 | 0.41 | YES
17 | CREBBP | CREBBP | CREBBP | 5599 | 0.064 | 0.42 | YES
18 | KAT2B | KAT2B | KAT2B | 5825 | 0.059 | 0.42 | YES
19 | EP300 | EP300 | EP300 | 5906 | 0.057 | 0.43 | YES
20 | HEYL | HEYL | HEYL | 6272 | 0.048 | 0.42 | NO
21 | FBXW7 | FBXW7 | FBXW7 | 6548 | 0.042 | 0.42 | NO
22 | RBPJ | RBPJ | RBPJ | 6818 | 0.037 | 0.41 | NO
23 | HDAC10 | HDAC10 | HDAC10 | 6931 | 0.035 | 0.41 | NO
24 | HDAC2 | HDAC2 | HDAC2 | 7338 | 0.026 | 0.4 | NO
25 | HIF1A | HIF1A | HIF1A | 7342 | 0.026 | 0.4 | NO
26 | SKP1 | SKP1 | SKP1 | 7525 | 0.023 | 0.4 | NO
27 | HES5 | HES5 | HES5 | 7826 | 0.017 | 0.38 | NO
28 | HDAC8 | HDAC8 | HDAC8 | 7924 | 0.015 | 0.38 | NO
29 | HEY2 | HEY2 | HEY2 | 8335 | 0.0074 | 0.36 | NO
30 | RPS27A | RPS27A | RPS27A | 9002 | -0.0045 | 0.33 | NO
31 | TBL1X | TBL1X | TBL1X | 9567 | -0.014 | 0.3 | NO
32 | HDAC6 | HDAC6 | HDAC6 | 9927 | -0.021 | 0.28 | NO
33 | CUL1 | CUL1 | CUL1 | 10217 | -0.026 | 0.27 | NO
34 | HDAC9 | HDAC9 | HDAC9 | 10351 | -0.028 | 0.27 | NO
35 | UBA52 | UBA52 | UBA52 | 10586 | -0.033 | 0.27 | NO
36 | SNW1 | SNW1 | SNW1 | 10685 | -0.035 | 0.27 | NO
37 | HDAC3 | HDAC3 | HDAC3 | 11172 | -0.045 | 0.26 | NO
38 | CCNC | CCNC | CCNC | 11183 | -0.045 | 0.27 | NO
39 | HDAC1 | HDAC1 | HDAC1 | 11744 | -0.057 | 0.25 | NO
40 | RBX1 | RBX1 | RBX1 | 11908 | -0.06 | 0.25 | NO
41 | TBL1XR1 | TBL1XR1 | TBL1XR1 | 12105 | -0.065 | 0.26 | NO
42 | TLE3 | TLE3 | TLE3 | 12478 | -0.074 | 0.26 | NO
43 | MYC | MYC | MYC | 13449 | -0.1 | 0.23 | NO
44 | CDK8 | CDK8 | CDK8 | 14027 | -0.13 | 0.23 | NO

Figure S105. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID INTEGRIN3 PATHWAY.

Figure S106. Get High-res Image For the top 5 core enriched genes in the pathway: PID INTEGRIN3 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID RHOA REG PATHWAY

Table S54. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | MAML3 | MAML3 | MAML3 | 735 | 0.34 | 0.076 | YES
2 | MAMLD1 | MAMLD1 | MAMLD1 | 1011 | 0.3 | 0.16 | YES
3 | MAML2 | MAML2 | MAML2 | 1501 | 0.25 | 0.22 | YES
4 | NOTCH3 | NOTCH3 | NOTCH3 | 1554 | 0.25 | 0.3 | YES
5 | CCND1 | CCND1 | CCND1 | 1727 | 0.23 | 0.37 | YES
6 | TP53 | TP53 | TP53 | 3221 | 0.14 | 0.34 | YES
7 | EIF2C2 | EIF2C2 | EIF2C2 | 3291 | 0.14 | 0.38 | YES
8 | NOTCH2 | NOTCH2 | NOTCH2 | 3650 | 0.12 | 0.4 | YES
9 | TNRC6C | TNRC6C | TNRC6C | 4910 | 0.082 | 0.36 | YES
10 | E2F3 | E2F3 | E2F3 | 5132 | 0.076 | 0.38 | YES
11 | MAML1 | MAML1 | MAML1 | 5273 | 0.073 | 0.39 | YES
12 | KAT2A | KAT2A | KAT2A | 5366 | 0.07 | 0.41 | YES
13 | CREBBP | CREBBP | CREBBP | 5599 | 0.064 | 0.42 | YES
14 | EIF2C4 | EIF2C4 | EIF2C4 | 5799 | 0.059 | 0.43 | YES
15 | KAT2B | KAT2B | KAT2B | 5825 | 0.059 | 0.45 | YES
16 | EP300 | EP300 | EP300 | 5906 | 0.057 | 0.46 | YES
17 | TNRC6A | TNRC6A | TNRC6A | 6407 | 0.045 | 0.45 | YES
18 | E2F1 | E2F1 | E2F1 | 6555 | 0.042 | 0.46 | YES
19 | JUN | JUN | JUN | 6765 | 0.038 | 0.46 | YES
20 | RBPJ | RBPJ | RBPJ | 6818 | 0.037 | 0.47 | YES
21 | TNRC6B | TNRC6B | TNRC6B | 8817 | -0.0011 | 0.36 | NO
22 | SNW1 | SNW1 | SNW1 | 10685 | -0.035 | 0.26 | NO
23 | EIF2C1 | EIF2C1 | EIF2C1 | 10809 | -0.037 | 0.27 | NO
24 | MOV10 | MOV10 | MOV10 | 12298 | -0.069 | 0.21 | NO
25 | NOTCH4 | NOTCH4 | NOTCH4 | 12559 | -0.077 | 0.22 | NO
26 | TFDP1 | TFDP1 | TFDP1 | 12753 | -0.083 | 0.24 | NO
27 | EIF2C3 | EIF2C3 | EIF2C3 | 14690 | -0.16 | 0.19 | NO

Figure S107. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID RHOA REG PATHWAY.

Figure S108. Get High-res Image For the top 5 core enriched genes in the pathway: PID RHOA REG PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID NECTIN PATHWAY

Table S55. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | ZFP37 | ZFP37 | ZFP37 | 61 | 0.7 | 0.01 | YES
2 | ZNF439 | ZNF439 | ZNF439 | 85 | 0.66 | 0.022 | YES
3 | ZNF433 | ZNF433 | ZNF433 | 110 | 0.62 | 0.032 | YES
4 | ZNF415 | ZNF415 | ZNF415 | 147 | 0.58 | 0.041 | YES
5 | NR3C2 | NR3C2 | NR3C2 | 171 | 0.55 | 0.05 | YES
6 | ZFP2 | ZFP2 | ZFP2 | 195 | 0.53 | 0.06 | YES
7 | ESRRG | ESRRG | ESRRG | 226 | 0.51 | 0.068 | YES
8 | ZNF577 | ZNF577 | ZNF577 | 229 | 0.51 | 0.077 | YES
9 | NR5A2 | NR5A2 | NR5A2 | 242 | 0.5 | 0.086 | YES
10 | ZNF382 | ZNF382 | ZNF382 | 288 | 0.48 | 0.093 | YES
11 | ZNF582 | ZNF582 | ZNF582 | 302 | 0.47 | 0.1 | YES
12 | ZNF454 | ZNF454 | ZNF454 | 357 | 0.45 | 0.11 | YES
13 | ZNF649 | ZNF649 | ZNF649 | 459 | 0.41 | 0.11 | YES
14 | ZNF30 | ZNF30 | ZNF30 | 476 | 0.41 | 0.12 | YES
15 | ZNF347 | ZNF347 | ZNF347 | 487 | 0.4 | 0.12 | YES
16 | ZNF10 | ZNF10 | ZNF10 | 546 | 0.39 | 0.13 | YES
17 | CTGF | CTGF | CTGF | 548 | 0.39 | 0.14 | YES
18 | ZNF625 | ZNF625 | ZNF625 | 549 | 0.39 | 0.14 | YES
19 | ZNF214 | ZNF214 | ZNF214 | 551 | 0.39 | 0.15 | YES
20 | ZNF287 | ZNF287 | ZNF287 | 600 | 0.38 | 0.15 | YES
21 | ZNF418 | ZNF418 | ZNF418 | 653 | 0.36 | 0.16 | YES
22 | ZNF641 | ZNF641 | ZNF641 | 656 | 0.36 | 0.16 | YES
23 | ZNF540 | ZNF540 | ZNF540 | 684 | 0.35 | 0.17 | YES
24 | ZNF620 | ZNF620 | ZNF620 | 702 | 0.35 | 0.18 | YES
25 | ZNF528 | ZNF528 | ZNF528 | 715 | 0.35 | 0.18 | YES
26 | MAML3 | MAML3 | MAML3 | 735 | 0.34 | 0.19 | YES
27 | WWTR1 | WWTR1 | WWTR1 | 778 | 0.34 | 0.19 | YES
28 | ZNF425 | ZNF425 | ZNF425 | 796 | 0.34 | 0.2 | YES
29 | ZIK1 | ZIK1 | ZIK1 | 800 | 0.34 | 0.2 | YES
30 | ZNF615 | ZNF615 | ZNF615 | 824 | 0.33 | 0.21 | YES
31 | ZNF354C | ZNF354C | ZNF354C | 857 | 0.32 | 0.21 | YES
32 | E2F5 | E2F5 | E2F5 | 896 | 0.32 | 0.22 | YES
33 | ZNF485 | ZNF485 | ZNF485 | 961 | 0.31 | 0.22 | YES
34 | SERPINE1 | SERPINE1 | SERPINE1 | 997 | 0.3 | 0.22 | YES
35 | ZNF619 | ZNF619 | ZNF619 | 998 | 0.3 | 0.23 | YES
36 | MAMLD1 | MAMLD1 | MAMLD1 | 1011 | 0.3 | 0.23 | YES
37 | RARG | RARG | RARG | 1051 | 0.3 | 0.24 | YES
38 | ZNF583 | ZNF583 | ZNF583 | 1152 | 0.29 | 0.24 | YES
39 | ZNF141 | ZNF141 | ZNF141 | 1169 | 0.29 | 0.24 | YES
40 | ZNF426 | ZNF426 | ZNF426 | 1253 | 0.28 | 0.24 | YES
41 | ZNF643 | ZNF643 | ZNF643 | 1333 | 0.27 | 0.24 | YES
42 | ZNF442 | ZNF442 | ZNF442 | 1363 | 0.27 | 0.25 | YES
43 | ZNF154 | ZNF154 | ZNF154 | 1380 | 0.26 | 0.25 | YES
44 | ZNF596 | ZNF596 | ZNF596 | 1414 | 0.26 | 0.25 | YES
45 | ZNF192 | ZNF192 | ZNF192 | 1455 | 0.26 | 0.26 | YES
46 | MAML2 | MAML2 | MAML2 | 1501 | 0.25 | 0.26 | YES
47 | ZNF157 | ZNF157 | ZNF157 | 1523 | 0.25 | 0.26 | YES
48 | ZNF642 | ZNF642 | ZNF642 | 1535 | 0.25 | 0.27 | YES
49 | SMAD7 | SMAD7 | SMAD7 | 1537 | 0.25 | 0.27 | YES
50 | ZNF285 | ZNF285 | ZNF285 | 1546 | 0.25 | 0.28 | YES
51 | ZNF250 | ZNF250 | ZNF250 | 1551 | 0.25 | 0.28 | YES
52 | NOTCH3 | NOTCH3 | NOTCH3 | 1554 | 0.25 | 0.28 | YES
53 | ZNF585B | ZNF585B | ZNF585B | 1595 | 0.24 | 0.29 | YES
54 | ZNF286A | ZNF286A | ZNF286A | 1607 | 0.24 | 0.29 | YES
55 | ZNF519 | ZNF519 | ZNF519 | 1641 | 0.24 | 0.29 | YES
56 | ZNF215 | ZNF215 | ZNF215 | 1670 | 0.24 | 0.3 | YES
57 | TEAD2 | TEAD2 | TEAD2 | 1680 | 0.24 | 0.3 | YES
58 | ZNF563 | ZNF563 | ZNF563 | 1689 | 0.23 | 0.3 | YES
59 | ZKSCAN4 | ZKSCAN4 | ZKSCAN4 | 1702 | 0.23 | 0.31 | YES
60 | ZNF614 | ZNF614 | ZNF614 | 1717 | 0.23 | 0.31 | YES
61 | ZNF483 | ZNF483 | ZNF483 | 1734 | 0.23 | 0.32 | YES
62 | ZNF514 | ZNF514 | ZNF514 | 1791 | 0.22 | 0.32 | YES
63 | ZNF266 | ZNF266 | ZNF266 | 1802 | 0.22 | 0.32 | YES
64 | ZKSCAN3 | ZKSCAN3 | ZKSCAN3 | 1838 | 0.22 | 0.32 | YES
65 | ZKSCAN1 | ZKSCAN1 | ZKSCAN1 | 1935 | 0.21 | 0.32 | YES
66 | ZNF569 | ZNF569 | ZNF569 | 1963 | 0.21 | 0.32 | YES
67 | ZNF613 | ZNF613 | ZNF613 | 1967 | 0.21 | 0.33 | YES
68 | NR2E3 | NR2E3 | NR2E3 | 2001 | 0.21 | 0.33 | YES
69 | ZNF571 | ZNF571 | ZNF571 | 2032 | 0.21 | 0.33 | YES
70 | ZNF599 | ZNF599 | ZNF599 | 2034 | 0.21 | 0.34 | YES
71 | TEAD3 | TEAD3 | TEAD3 | 2156 | 0.2 | 0.33 | YES
72 | ZNF773 | ZNF773 | ZNF773 | 2157 | 0.2 | 0.34 | YES
73 | ZNF221 | ZNF221 | ZNF221 | 2171 | 0.2 | 0.34 | YES
74 | ZNF169 | ZNF169 | ZNF169 | 2175 | 0.2 | 0.34 | YES
75 | ZNF610 | ZNF610 | ZNF610 | 2176 | 0.2 | 0.35 | YES
76 | ZNF419 | ZNF419 | ZNF419 | 2180 | 0.2 | 0.35 | YES
77 | ZNF585A | ZNF585A | ZNF585A | 2195 | 0.2 | 0.36 | YES
78 | ZNF559 | ZNF559 | ZNF559 | 2254 | 0.19 | 0.36 | YES
79 | TBX5 | TBX5 | TBX5 | 2356 | 0.19 | 0.35 | YES
80 | ZNF607 | ZNF607 | ZNF607 | 2368 | 0.19 | 0.36 | YES
81 | ZNF432 | ZNF432 | ZNF432 | 2407 | 0.18 | 0.36 | YES
82 | ZNF175 | ZNF175 | ZNF175 | 2417 | 0.18 | 0.36 | YES
83 | ZNF517 | ZNF517 | ZNF517 | 2430 | 0.18 | 0.36 | YES
84 | ZNF167 | ZNF167 | ZNF167 | 2440 | 0.18 | 0.37 | YES
85 | ZNF560 | ZNF560 | ZNF560 | 2465 | 0.18 | 0.37 | YES
86 | ZNF611 | ZNF611 | ZNF611 | 2474 | 0.18 | 0.37 | YES
87 | TGIF2 | TGIF2 | TGIF2 | 2482 | 0.18 | 0.37 | YES
88 | ZNF600 | ZNF600 | ZNF600 | 2516 | 0.18 | 0.38 | YES
89 | NR1D1 | NR1D1 | NR1D1 | 2527 | 0.18 | 0.38 | YES
90 | ZNF223 | ZNF223 | ZNF223 | 2541 | 0.18 | 0.38 | YES
91 | ZNF496 | ZNF496 | ZNF496 | 2563 | 0.17 | 0.38 | YES
92 | ZNF546 | ZNF546 | ZNF546 | 2569 | 0.17 | 0.39 | YES
93 | ZFP28 | ZFP28 | ZFP28 | 2708 | 0.16 | 0.38 | YES
94 | NR1D2 | NR1D2 | NR1D2 | 2749 | 0.16 | 0.38 | YES
95 | ZNF471 | ZNF471 | ZNF471 | 2779 | 0.16 | 0.38 | YES
96 | SMURF2 | SMURF2 | SMURF2 | 2784 | 0.16 | 0.39 | YES
97 | ZNF211 | ZNF211 | ZNF211 | 2839 | 0.16 | 0.39 | YES
98 | ZNF25 | ZNF25 | ZNF25 | 2849 | 0.16 | 0.39 | YES
99 | ZNF20 | ZNF20 | ZNF20 | 2851 | 0.16 | 0.39 | YES
100 | ZNF33B | ZNF33B | ZNF33B | 2864 | 0.16 | 0.4 | YES
101 | NCOA2 | NCOA2 | NCOA2 | 2874 | 0.16 | 0.4 | YES
102 | ZNF493 | ZNF493 | ZNF493 | 2878 | 0.16 | 0.4 | YES
103 | ZNF256 | ZNF256 | ZNF256 | 2879 | 0.16 | 0.4 | YES
104 | ZNF225 | ZNF225 | ZNF225 | 2880 | 0.16 | 0.41 | YES
105 | ZNF443 | ZNF443 | ZNF443 | 2882 | 0.16 | 0.41 | YES
106 | ZNF222 | ZNF222 | ZNF222 | 2889 | 0.16 | 0.41 | YES
107 | ZNF551 | ZNF551 | ZNF551 | 2915 | 0.16 | 0.41 | YES
108 | ZNF337 | ZNF337 | ZNF337 | 2974 | 0.15 | 0.41 | YES
109 | ZNF627 | ZNF627 | ZNF627 | 2982 | 0.15 | 0.42 | YES
110 | ZNF565 | ZNF565 | ZNF565 | 3002 | 0.15 | 0.42 | YES
111 | ZNF343 | ZNF343 | ZNF343 | 3022 | 0.15 | 0.42 | YES
112 | ZNF300 | ZNF300 | ZNF300 | 3064 | 0.15 | 0.42 | YES
113 | MED30 | MED30 | MED30 | 3083 | 0.14 | 0.42 | YES
114 | ZFP112 | ZFP112 | ZFP112 | 3086 | 0.14 | 0.42 | YES
115 | ZNF605 | ZNF605 | ZNF605 | 3102 | 0.14 | 0.43 | YES
116 | ZNF606 | ZNF606 | ZNF606 | 3139 | 0.14 | 0.43 | YES
117 | NR0B2 | NR0B2 | NR0B2 | 3144 | 0.14 | 0.43 | YES
118 | ZNF566 | ZNF566 | ZNF566 | 3165 | 0.14 | 0.43 | YES
119 | SKIL | SKIL | SKIL | 3199 | 0.14 | 0.43 | YES
120 | RORA | RORA | RORA | 3204 | 0.14 | 0.43 | YES
121 | PGR | PGR | PGR | 3227 | 0.14 | 0.44 | YES
122 | ZNF416 | ZNF416 | ZNF416 | 3247 | 0.14 | 0.44 | YES
123 | ZNF441 | ZNF441 | ZNF441 | 3259 | 0.14 | 0.44 | YES
124 | MED12 | MED12 | MED12 | 3261 | 0.14 | 0.44 | YES
125 | ZNF570 | ZNF570 | ZNF570 | 3274 | 0.14 | 0.44 | YES
126 | RBL1 | RBL1 | RBL1 | 3296 | 0.14 | 0.44 | YES
127 | ZNF595 | ZNF595 | ZNF595 | 3301 | 0.14 | 0.45 | YES
128 | SKI | SKI | SKI | 3341 | 0.14 | 0.45 | YES
129 | ZNF500 | ZNF500 | ZNF500 | 3502 | 0.13 | 0.44 | YES
130 | ZNF320 | ZNF320 | ZNF320 | 3512 | 0.13 | 0.44 | YES
131 | JUNB | JUNB | JUNB | 3534 | 0.13 | 0.44 | YES
132 | ZNF708 | ZNF708 | ZNF708 | 3561 | 0.13 | 0.44 | YES
133 | ZNF274 | ZNF274 | ZNF274 | 3602 | 0.12 | 0.44 | YES
134 | NOTCH2 | NOTCH2 | NOTCH2 | 3650 | 0.12 | 0.44 | YES
135 | ZNF184 | ZNF184 | ZNF184 | 3676 | 0.12 | 0.45 | YES
136 | ZNF420 | ZNF420 | ZNF420 | 3681 | 0.12 | 0.45 | YES
137 | ZNF235 | ZNF235 | ZNF235 | 3715 | 0.12 | 0.45 | YES
138 | TEAD1 | TEAD1 | TEAD1 | 3761 | 0.12 | 0.45 | YES
139 | ZNF33A | ZNF33A | ZNF33A | 3762 | 0.12 | 0.45 | YES
140 | PARP1 | PARP1 | PARP1 | 3793 | 0.12 | 0.45 | YES
141 | ZNF529 | ZNF529 | ZNF529 | 3848 | 0.12 | 0.45 | YES
142 | ZNF140 | ZNF140 | ZNF140 | 3853 | 0.12 | 0.45 | YES
143 | ZNF331 | ZNF331 | ZNF331 | 3894 | 0.11 | 0.45 | YES
144 | SMARCD3 | SMARCD3 | SMARCD3 | 3993 | 0.11 | 0.45 | YES
145 | ZNF589 | ZNF589 | ZNF589 | 3999 | 0.11 | 0.45 | YES
146 | ZNF37A | ZNF37A | ZNF37A | 4033 | 0.11 | 0.45 | YES
147 | ZNF543 | ZNF543 | ZNF543 | 4048 | 0.11 | 0.45 | YES
148 | ZNF354B | ZNF354B | ZNF354B | 4054 | 0.11 | 0.45 | YES
149 | PRIC285 | PRIC285 | PRIC285 | 4099 | 0.11 | 0.45 | YES
150 | ZNF45 | ZNF45 | ZNF45 | 4105 | 0.11 | 0.46 | YES
151 | HNF4A | HNF4A | HNF4A | 4139 | 0.11 | 0.46 | YES
152 | ZNF621 | ZNF621 | ZNF621 | 4144 | 0.1 | 0.46 | YES
153 | CDK9 | CDK9 | CDK9 | 4209 | 0.1 | 0.46 | YES
154 | ZNF43 | ZNF43 | ZNF43 | 4239 | 0.1 | 0.46 | YES
155 | ZNF398 | ZNF398 | ZNF398 | 4292 | 0.1 | 0.46 | YES
156 | ZNF552 | ZNF552 | ZNF552 | 4302 | 0.1 | 0.46 | YES
157 | THRB | THRB | THRB | 4311 | 0.1 | 0.46 | YES
158 | ZNF510 | ZNF510 | ZNF510 | 4333 | 0.1 | 0.46 | YES
159 | CDKN2B | CDKN2B | CDKN2B | 4391 | 0.098 | 0.46 | YES
160 | HNF4G | HNF4G | HNF4G | 4398 | 0.097 | 0.46 | YES
161 | NR6A1 | NR6A1 | NR6A1 | 4514 | 0.094 | 0.45 | YES
162 | MED20 | MED20 | MED20 | 4526 | 0.093 | 0.46 | YES
163 | ZNF28 | ZNF28 | ZNF28 | 4552 | 0.092 | 0.46 | YES
164 | ZNF417 | ZNF417 | ZNF417 | 4614 | 0.091 | 0.45 | YES
165 | ZNF350 | ZNF350 | ZNF350 | 4628 | 0.09 | 0.46 | YES
166 | NCOR2 | NCOR2 | NCOR2 | 4640 | 0.09 | 0.46 | YES
167 | ZNF624 | ZNF624 | ZNF624 | 4653 | 0.09 | 0.46 | YES
168 | ZNF383 | ZNF383 | ZNF383 | 4680 | 0.089 | 0.46 | YES
169 | ZNF548 | ZNF548 | ZNF548 | 4697 | 0.088 | 0.46 | YES
170 | ZNF234 | ZNF234 | ZNF234 | 4709 | 0.088 | 0.46 | YES
171 | ZNF440 | ZNF440 | ZNF440 | 4714 | 0.088 | 0.46 | YES
172 | ZNF160 | ZNF160 | ZNF160 | 4732 | 0.087 | 0.46 | YES
173 | NR4A2 | NR4A2 | NR4A2 | 4740 | 0.087 | 0.46 | YES
174 | ZNF205 | ZNF205 | ZNF205 | 4757 | 0.087 | 0.46 | YES
175 | ZNF2 | ZNF2 | ZNF2 | 4798 | 0.085 | 0.46 | YES
176 | SMAD4 | SMAD4 | SMAD4 | 4853 | 0.084 | 0.46 | YES
177 | ZNF468 | ZNF468 | ZNF468 | 4878 | 0.083 | 0.46 | YES
178 | ZNF304 | ZNF304 | ZNF304 | 4882 | 0.083 | 0.46 | YES
179 | ZNF561 | ZNF561 | ZNF561 | 4913 | 0.082 | 0.46 | YES
180 | ZNF558 | ZNF558 | ZNF558 | 4924 | 0.082 | 0.46 | YES
181 | ZNF197 | ZNF197 | ZNF197 | 4931 | 0.082 | 0.47 | YES
182 | ZNF334 | ZNF334 | ZNF334 | 4960 | 0.081 | 0.46 | YES
183 | ZNF100 | ZNF100 | ZNF100 | 4985 | 0.08 | 0.47 | YES
184 | ZNF555 | ZNF555 | ZNF555 | 5004 | 0.08 | 0.47 | YES
185 | ZNF248 | ZNF248 | ZNF248 | 5068 | 0.078 | 0.46 | NO
186 | ZNF333 | ZNF333 | ZNF333 | 5084 | 0.078 | 0.46 | NO
187 | MAML1 | MAML1 | MAML1 | 5273 | 0.073 | 0.46 | NO
188 | NCOA3 | NCOA3 | NCOA3 | 5317 | 0.072 | 0.46 | NO
189 | ZNF311 | ZNF311 | ZNF311 | 5360 | 0.07 | 0.45 | NO
190 | KAT2A | KAT2A | KAT2A | 5366 | 0.07 | 0.46 | NO
191 | NCOR1 | NCOR1 | NCOR1 | 5489 | 0.067 | 0.45 | NO
192 | RARA | RARA | RARA | 5571 | 0.064 | 0.45 | NO
193 | CCNT1 | CCNT1 | CCNT1 | 5577 | 0.064 | 0.45 | NO
194 | CREBBP | CREBBP | CREBBP | 5599 | 0.064 | 0.45 | NO
195 | ZNF213 | ZNF213 | ZNF213 | 5628 | 0.063 | 0.45 | NO
196 | SP1 | SP1 | SP1 | 5641 | 0.062 | 0.45 | NO
197 | TGS1 | TGS1 | TGS1 | 5823 | 0.059 | 0.44 | NO
198 | KAT2B | KAT2B | KAT2B | 5825 | 0.059 | 0.44 | NO
199 | ZNF254 | ZNF254 | ZNF254 | 5944 | 0.056 | 0.43 | NO
200 | NCOA6 | NCOA6 | NCOA6 | 5966 | 0.055 | 0.43 | NO
201 | ZNF557 | ZNF557 | ZNF557 | 6025 | 0.054 | 0.43 | NO
202 | ZNF230 | ZNF230 | ZNF230 | 6051 | 0.053 | 0.43 | NO
203 | ZNF658 | ZNF658 | ZNF658 | 6056 | 0.053 | 0.43 | NO
204 | ZNF212 | ZNF212 | ZNF212 | 6100 | 0.052 | 0.43 | NO
205 | ZNF26 | ZNF26 | ZNF26 | 6123 | 0.052 | 0.43 | NO
206 | ZNF224 | ZNF224 | ZNF224 | 6182 | 0.05 | 0.43 | NO
207 | ZNF564 | ZNF564 | ZNF564 | 6313 | 0.047 | 0.42 | NO
208 | PPM1A | PPM1A | PPM1A | 6327 | 0.047 | 0.42 | NO
209 | ZNF264 | ZNF264 | ZNF264 | 6432 | 0.044 | 0.42 | NO
210 | ZNF597 | ZNF597 | ZNF597 | 6446 | 0.044 | 0.42 | NO
211 | RXRB | RXRB | RXRB | 6480 | 0.044 | 0.42 | NO
212 | TEAD4 | TEAD4 | TEAD4 | 6584 | 0.042 | 0.41 | NO
213 | ZNF484 | ZNF484 | ZNF484 | 6641 | 0.04 | 0.41 | NO
214 | MED17 | MED17 | MED17 | 6645 | 0.04 | 0.41 | NO
215 | ZNF282 | ZNF282 | ZNF282 | 6663 | 0.04 | 0.41 | NO
216 | ZNF354A | ZNF354A | ZNF354A | 6769 | 0.038 | 0.4 | NO
217 | YAP1 | YAP1 | YAP1 | 6796 | 0.037 | 0.4 | NO
218 | RBPJ | RBPJ | RBPJ | 6818 | 0.037 | 0.4 | NO
219 | NR1H3 | NR1H3 | NR1H3 | 6854 | 0.036 | 0.4 | NO
220 | ZNF227 | ZNF227 | ZNF227 | 6915 | 0.035 | 0.4 | NO
221 | ZNF14 | ZNF14 | ZNF14 | 6917 | 0.035 | 0.4 | NO
222 | TRIM33 | TRIM33 | TRIM33 | 6960 | 0.034 | 0.4 | NO
223 | ZNF530 | ZNF530 | ZNF530 | 6995 | 0.033 | 0.4 | NO
224 | SMAD2 | SMAD2 | SMAD2 | 7026 | 0.032 | 0.39 | NO
225 | ZNF17 | ZNF17 | ZNF17 | 7094 | 0.031 | 0.39 | NO
226 | ZNF434 | ZNF434 | ZNF434 | 7116 | 0.03 | 0.39 | NO
227 | ZNF584 | ZNF584 | ZNF584 | 7145 | 0.03 | 0.39 | NO
228 | MED31 | MED31 | MED31 | 7167 | 0.03 | 0.39 | NO
229 | PPARD | PPARD | PPARD | 7397 | 0.025 | 0.38 | NO
230 | MED14 | MED14 | MED14 | 7448 | 0.024 | 0.37 | NO
231 | ZNF567 | ZNF567 | ZNF567 | 7488 | 0.023 | 0.37 | NO
232 | ZNF202 | ZNF202 | ZNF202 | 7503 | 0.023 | 0.37 | NO
233 | ZNF445 | ZNF445 | ZNF445 | 7559 | 0.022 | 0.37 | NO
234 | UBE2D3 | UBE2D3 | UBE2D3 | 7577 | 0.022 | 0.37 | NO
235 | CCNT2 | CCNT2 | CCNT2 | 7584 | 0.022 | 0.37 | NO
236 | ZNF490 | ZNF490 | ZNF490 | 7707 | 0.019 | 0.36 | NO
237 | NR4A1 | NR4A1 | NR4A1 | 7727 | 0.019 | 0.36 | NO
238 | ZNF446 | ZNF446 | ZNF446 | 7757 | 0.018 | 0.36 | NO
239 | TGIF1 | TGIF1 | TGIF1 | 7809 | 0.017 | 0.36 | NO
240 | ZNF587 | ZNF587 | ZNF587 | 7836 | 0.017 | 0.36 | NO
241 | ZNF430 | ZNF430 | ZNF430 | 7890 | 0.016 | 0.35 | NO
242 | ZNF473 | ZNF473 | ZNF473 | 7893 | 0.016 | 0.35 | NO
243 | ZNF3 | ZNF3 | ZNF3 | 7970 | 0.014 | 0.35 | NO
244 | ZNF136 | ZNF136 | ZNF136 | 8049 | 0.013 | 0.35 | NO
245 | NR2F6 | NR2F6 | NR2F6 | 8181 | 0.01 | 0.34 | NO
246 | MED23 | MED23 | MED23 | 8240 | 0.0091 | 0.34 | NO
247 | ZNF208 | ZNF208 | ZNF208 | 8420 | 0.0057 | 0.33 | NO
248 | ZNF180 | ZNF180 | ZNF180 | 8538 | 0.0034 | 0.32 | NO
249 | RXRA | RXRA | RXRA | 8545 | 0.0033 | 0.32 | NO
250 | MED1 | MED1 | MED1 | 8591 | 0.0027 | 0.32 | NO
251 | USP9X | USP9X | USP9X | 8612 | 0.0025 | 0.32 | NO
252 | ZNF18 | ZNF18 | ZNF18 | 8650 | 0.0018 | 0.31 | NO
253 | SMAD3 | SMAD3 | SMAD3 | 8685 | 0.0011 | 0.31 | NO
254 | ZNF498 | ZNF498 | ZNF498 | 8761 | -0.00015 | 0.31 | NO
255 | TRIM28 | TRIM28 | TRIM28 | 8979 | -0.0041 | 0.3 | NO
256 | NR2C2AP | NR2C2AP | NR2C2AP | 8982 | -0.0042 | 0.3 | NO
257 | RPS27A | RPS27A | RPS27A | 9002 | -0.0045 | 0.29 | NO
258 | ZNF155 | ZNF155 | ZNF155 | 9033 | -0.0051 | 0.29 | NO
259 | ZNF317 | ZNF317 | ZNF317 | 9071 | -0.0059 | 0.29 | NO
260 | NCOA1 | NCOA1 | NCOA1 | 9212 | -0.0085 | 0.28 | NO
261 | ZNF263 | ZNF263 | ZNF263 | 9272 | -0.0095 | 0.28 | NO
262 | MED25 | MED25 | MED25 | 9295 | -0.0098 | 0.28 | NO
263 | MED24 | MED24 | MED24 | 9317 | -0.01 | 0.28 | NO
264 | ZNF616 | ZNF616 | ZNF616 | 9400 | -0.012 | 0.27 | NO
265 | ZNF547 | ZNF547 | ZNF547 | 9481 | -0.013 | 0.27 | NO
266 | MED16 | MED16 | MED16 | 9509 | -0.014 | 0.27 | NO
267 | TBL1X | TBL1X | TBL1X | 9567 | -0.014 | 0.26 | NO
268 | ZNF655 | ZNF655 | ZNF655 | 9899 | -0.02 | 0.25 | NO
269 | UBE2D1 | UBE2D1 | UBE2D1 | 9908 | -0.02 | 0.25 | NO
270 | MED15 | MED15 | MED15 | 9977 | -0.022 | 0.24 | NO
271 | ZNF19 | ZNF19 | ZNF19 | 9991 | -0.022 | 0.24 | NO
272 | ZNF226 | ZNF226 | ZNF226 | 10055 | -0.023 | 0.24 | NO
273 | ZNF324 | ZNF324 | ZNF324 | 10146 | -0.024 | 0.24 | NO
274 | NR2F1 | NR2F1 | NR2F1 | 10270 | -0.027 | 0.23 | NO
275 | UBA52 | UBA52 | UBA52 | 10586 | -0.033 | 0.21 | NO
276 | MED27 | MED27 | MED27 | 10646 | -0.034 | 0.21 | NO
277 | SNW1 | SNW1 | SNW1 | 10685 | -0.035 | 0.21 | NO
278 | MEN1 | MEN1 | MEN1 | 10711 | -0.036 | 0.21 | NO
279 | MED26 | MED26 | MED26 | 10822 | -0.038 | 0.2 | NO
280 | ZNF436 | ZNF436 | ZNF436 | 10860 | -0.038 | 0.2 | NO
281 | NRBF2 | NRBF2 | NRBF2 | 10908 | -0.039 | 0.2 | NO
282 | NRBP1 | NRBP1 | NRBP1 | 11098 | -0.043 | 0.19 | NO
283 | NR1H2 | NR1H2 | NR1H2 | 11101 | -0.043 | 0.19 | NO
284 | ZNF394 | ZNF394 | ZNF394 | 11174 | -0.045 | 0.19 | NO
285 | CCNC | CCNC | CCNC | 11183 | -0.045 | 0.19 | NO
286 | ZNF480 | ZNF480 | ZNF480 | 11197 | -0.045 | 0.19 | NO
287 | VDR | VDR | VDR | 11482 | -0.051 | 0.17 | NO
288 | NR3C1 | NR3C1 | NR3C1 | 11553 | -0.052 | 0.17 | NO
289 | ZNF460 | ZNF460 | ZNF460 | 11729 | -0.056 | 0.16 | NO
290 | HDAC1 | HDAC1 | HDAC1 | 11744 | -0.057 | 0.16 | NO
291 | ZNF431 | ZNF431 | ZNF431 | 11810 | -0.058 | 0.16 | NO
292 | ZFP90 | ZFP90 | ZFP90 | 12077 | -0.064 | 0.14 | NO
293 | TBL1XR1 | TBL1XR1 | TBL1XR1 | 12105 | -0.065 | 0.14 | NO
294 | MED8 | MED8 | MED8 | 12144 | -0.066 | 0.14 | NO
295 | ZNF544 | ZNF544 | ZNF544 | 12228 | -0.068 | 0.14 | NO
296 | ZNF12 | ZNF12 | ZNF12 | 12246 | -0.068 | 0.14 | NO
297 | ZKSCAN5 | ZKSCAN5 | ZKSCAN5 | 12371 | -0.072 | 0.13 | NO
298 | THRA | THRA | THRA | 12482 | -0.075 | 0.13 | NO
299 | NOTCH4 | NOTCH4 | NOTCH4 | 12559 | -0.077 | 0.13 | NO
300 | ZNF23 | ZNF23 | ZNF23 | 12660 | -0.08 | 0.12 | NO
301 | TFDP1 | TFDP1 | TFDP1 | 12753 | -0.083 | 0.12 | NO
302 | ZNF200 | ZNF200 | ZNF200 | 12857 | -0.086 | 0.12 | NO
303 | MED7 | MED7 | MED7 | 12973 | -0.089 | 0.11 | NO
304 | ZNF506 | ZNF506 | ZNF506 | 13028 | -0.091 | 0.11 | NO
305 | ZNF189 | ZNF189 | ZNF189 | 13263 | -0.099 | 0.098 | NO
306 | NR0B1 | NR0B1 | NR0B1 | 13339 | -0.1 | 0.095 | NO
307 | NR4A3 | NR4A3 | NR4A3 | 13365 | -0.1 | 0.096 | NO
308 | MYC | MYC | MYC | 13449 | -0.1 | 0.093 | NO
309 | MED10 | MED10 | MED10 | 13505 | -0.11 | 0.092 | NO
310 | ESRRA | ESRRA | ESRRA | 13529 | -0.11 | 0.093 | NO
311 | MED4 | MED4 | MED4 | 13739 | -0.12 | 0.083 | NO
312 | ZNF267 | ZNF267 | ZNF267 | 13752 | -0.12 | 0.085 | NO
313 | ZNF138 | ZNF138 | ZNF138 | 13825 | -0.12 | 0.083 | NO
314 | RORC | RORC | RORC | 14025 | -0.13 | 0.074 | NO
315 | CDK8 | CDK8 | CDK8 | 14027 | -0.13 | 0.077 | NO
316 | MED6 | MED6 | MED6 | 14172 | -0.13 | 0.071 | NO
317 | NR5A1 | NR5A1 | NR5A1 | 14201 | -0.13 | 0.072 | NO
318 | NR2E1 | NR2E1 | NR2E1 | 14204 | -0.13 | 0.075 | NO
319 | ZFP1 | ZFP1 | ZFP1 | 14270 | -0.14 | 0.074 | NO
320 | PPARA | PPARA | PPARA | 14351 | -0.14 | 0.072 | NO
321 | ZNF273 | ZNF273 | ZNF273 | 14471 | -0.15 | 0.068 | NO
322 | ZNF101 | ZNF101 | ZNF101 | 14598 | -0.16 | 0.064 | NO
323 | E2F4 | E2F4 | E2F4 | 15123 | -0.19 | 0.038 | NO
324 | ZNF92 | ZNF92 | ZNF92 | 15276 | -0.2 | 0.033 | NO
325 | NR1I3 | NR1I3 | NR1I3 | 15496 | -0.22 | 0.025 | NO
326 | RUNX2 | RUNX2 | RUNX2 | 15809 | -0.25 | 0.012 | NO
327 | RORB | RORB | RORB | 16293 | -0.3 | -0.0092 | NO
328 | ESR2 | ESR2 | ESR2 | 16407 | -0.32 | -0.0095 | NO
329 | PPARG | PPARG | PPARG | 16731 | -0.36 | -0.021 | NO
330 | ZNF98 | ZNF98 | ZNF98 | 16861 | -0.39 | -0.02 | NO
331 | ESRRB | ESRRB | ESRRB | 17142 | -0.44 | -0.028 | NO
332 | RXRG | RXRG | RXRG | 17163 | -0.44 | -0.02 | NO
333 | AR | AR | AR | 17480 | -0.51 | -0.028 | NO
334 | ZNF492 | ZNF492 | ZNF492 | 17540 | -0.53 | -0.021 | NO
335 | NPPA | NPPA | NPPA | 17698 | -0.58 | -0.019 | NO
336 | ZNF114 | ZNF114 | ZNF114 | 17811 | -0.64 | -0.013 | NO
337 | ESR1 | ESR1 | ESR1 | 17962 | -0.72 | -0.0078 | NO
338 | NR1I2 | NR1I2 | NR1I2 | 18062 | -0.84 | 0.0029 | NO

Figure S109. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID NECTIN PATHWAY.

Figure S110. Get High-res Image For the top 5 core enriched genes in the pathway: PID NECTIN PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID TGFBRPATHWAY

Table S56. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | WWTR1 | WWTR1 | WWTR1 | 778 | 0.34 | 0.05 | YES
2 | E2F5 | E2F5 | E2F5 | 896 | 0.32 | 0.13 | YES
3 | SERPINE1 | SERPINE1 | SERPINE1 | 997 | 0.3 | 0.21 | YES
4 | SMAD7 | SMAD7 | SMAD7 | 1537 | 0.25 | 0.25 | YES
5 | TGIF2 | TGIF2 | TGIF2 | 2482 | 0.18 | 0.24 | YES
6 | SMURF2 | SMURF2 | SMURF2 | 2784 | 0.16 | 0.27 | YES
7 | SKIL | SKIL | SKIL | 3199 | 0.14 | 0.29 | YES
8 | RBL1 | RBL1 | RBL1 | 3296 | 0.14 | 0.32 | YES
9 | SKI | SKI | SKI | 3341 | 0.14 | 0.35 | YES
10 | JUNB | JUNB | JUNB | 3534 | 0.13 | 0.38 | YES
11 | PARP1 | PARP1 | PARP1 | 3793 | 0.12 | 0.4 | YES
12 | CDK9 | CDK9 | CDK9 | 4209 | 0.1 | 0.4 | YES
13 | CDKN2B | CDKN2B | CDKN2B | 4391 | 0.098 | 0.42 | YES
14 | NCOR2 | NCOR2 | NCOR2 | 4640 | 0.09 | 0.43 | YES
15 | SMAD4 | SMAD4 | SMAD4 | 4853 | 0.084 | 0.44 | YES
16 | NCOR1 | NCOR1 | NCOR1 | 5489 | 0.067 | 0.42 | YES
17 | CCNT1 | CCNT1 | CCNT1 | 5577 | 0.064 | 0.44 | YES
18 | SP1 | SP1 | SP1 | 5641 | 0.062 | 0.45 | YES
19 | PPM1A | PPM1A | PPM1A | 6327 | 0.047 | 0.42 | NO
20 | TRIM33 | TRIM33 | TRIM33 | 6960 | 0.034 | 0.4 | NO
21 | SMAD2 | SMAD2 | SMAD2 | 7026 | 0.032 | 0.4 | NO
22 | UBE2D3 | UBE2D3 | UBE2D3 | 7577 | 0.022 | 0.38 | NO
23 | CCNT2 | CCNT2 | CCNT2 | 7584 | 0.022 | 0.38 | NO
24 | TGIF1 | TGIF1 | TGIF1 | 7809 | 0.017 | 0.38 | NO
25 | USP9X | USP9X | USP9X | 8612 | 0.0025 | 0.33 | NO
26 | SMAD3 | SMAD3 | SMAD3 | 8685 | 0.0011 | 0.33 | NO
27 | RPS27A | RPS27A | RPS27A | 9002 | -0.0045 | 0.31 | NO
28 | UBE2D1 | UBE2D1 | UBE2D1 | 9908 | -0.02 | 0.27 | NO
29 | UBA52 | UBA52 | UBA52 | 10586 | -0.033 | 0.24 | NO
30 | MEN1 | MEN1 | MEN1 | 10711 | -0.036 | 0.24 | NO
31 | CCNC | CCNC | CCNC | 11183 | -0.045 | 0.23 | NO
32 | HDAC1 | HDAC1 | HDAC1 | 11744 | -0.057 | 0.22 | NO
33 | TFDP1 | TFDP1 | TFDP1 | 12753 | -0.083 | 0.18 | NO
34 | MYC | MYC | MYC | 13449 | -0.1 | 0.17 | NO
35 | CDK8 | CDK8 | CDK8 | 14027 | -0.13 | 0.18 | NO
36 | E2F4 | E2F4 | E2F4 | 15123 | -0.19 | 0.16 | NO

Figure S111. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID TGFBRPATHWAY.

Figure S112. Get High-res Image For the top 5 core enriched genes in the pathway: PID TGFBRPATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS

Table S57. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | PLEKHG6 | PLEKHG6 | PLEKHG6 | 329 | 0.46 | 0.056 | YES
2 | ARHGAP6 | ARHGAP6 | ARHGAP6 | 638 | 0.36 | 0.098 | YES
3 | OBSCN | OBSCN | OBSCN | 752 | 0.34 | 0.15 | YES
4 | VAV3 | VAV3 | VAV3 | 880 | 0.32 | 0.19 | YES
5 | ARHGAP8 | ARHGAP8 | ARHGAP8 | 907 | 0.32 | 0.24 | YES
6 | ARHGDIG | ARHGDIG | ARHGDIG | 1301 | 0.27 | 0.26 | YES
7 | ARHGEF2 | ARHGEF2 | ARHGEF2 | 1356 | 0.27 | 0.3 | YES
8 | ARAP3 | ARAP3 | ARAP3 | 1649 | 0.24 | 0.33 | YES
9 | NGEF | NGEF | NGEF | 2673 | 0.17 | 0.3 | YES
10 | ARHGEF11 | ARHGEF11 | ARHGEF11 | 2766 | 0.16 | 0.32 | YES
11 | RGNEF | RGNEF | RGNEF | 2860 | 0.16 | 0.34 | YES
12 | DLC1 | DLC1 | DLC1 | 3104 | 0.14 | 0.35 | YES
13 | NET1 | NET1 | NET1 | 3196 | 0.14 | 0.37 | YES
14 | ARHGEF5 | ARHGEF5 | ARHGEF5 | 3591 | 0.12 | 0.36 | YES
15 | ARHGEF18 | ARHGEF18 | ARHGEF18 | 3758 | 0.12 | 0.38 | YES
16 | ARHGEF17 | ARHGEF17 | ARHGEF17 | 4358 | 0.098 | 0.36 | YES
17 | ARHGAP4 | ARHGAP4 | ARHGAP4 | 4479 | 0.095 | 0.37 | YES
18 | FARP1 | FARP1 | FARP1 | 4629 | 0.09 | 0.37 | YES
19 | ABR | ABR | ABR | 4718 | 0.088 | 0.38 | YES
20 | SRGAP1 | SRGAP1 | SRGAP1 | 4765 | 0.086 | 0.39 | YES
21 | ARHGEF1 | ARHGEF1 | ARHGEF1 | 5169 | 0.075 | 0.38 | NO
22 | CDKN1B | CDKN1B | CDKN1B | 5325 | 0.072 | 0.39 | NO
23 | BCR | BCR | BCR | 5688 | 0.062 | 0.38 | NO
24 | ARHGEF10 | ARHGEF10 | ARHGEF10 | 6023 | 0.054 | 0.37 | NO
25 | ARHGAP5 | ARHGAP5 | ARHGAP5 | 7437 | 0.024 | 0.29 | NO
26 | ARHGEF12 | ARHGEF12 | ARHGEF12 | 7452 | 0.024 | 0.3 | NO
27 | MCF2L | MCF2L | MCF2L | 7720 | 0.019 | 0.28 | NO
28 | MYO9B | MYO9B | MYO9B | 8045 | 0.013 | 0.27 | NO
29 | RHOA | RHOA | RHOA | 8539 | 0.0034 | 0.24 | NO
30 | AKAP13 | AKAP13 | AKAP13 | 9028 | -0.0051 | 0.22 | NO
31 | ECT2 | ECT2 | ECT2 | 9139 | -0.0073 | 0.21 | NO
32 | VAV2 | VAV2 | VAV2 | 9149 | -0.0075 | 0.21 | NO
33 | ARHGEF10L | ARHGEF10L | ARHGEF10L | 9221 | -0.0086 | 0.21 | NO
34 | TRIO | TRIO | TRIO | 9344 | -0.011 | 0.2 | NO
35 | MCF2 | MCF2 | MCF2 | 10975 | -0.04 | 0.12 | NO
36 | ARAP1 | ARAP1 | ARAP1 | 11349 | -0.048 | 0.11 | NO
37 | ARHGDIA | ARHGDIA | ARHGDIA | 11519 | -0.052 | 0.11 | NO
38 | ARHGDIB | ARHGDIB | ARHGDIB | 14593 | -0.15 | -0.039 | NO
39 | ARHGEF3 | ARHGEF3 | ARHGEF3 | 14857 | -0.17 | -0.026 | NO
40 | OPHN1 | OPHN1 | OPHN1 | 14889 | -0.17 | -0.00016 | NO
41 | DEF6 | DEF6 | DEF6 | 15470 | -0.21 | 0.0025 | NO
42 | ARHGEF15 | ARHGEF15 | ARHGEF15 | 15491 | -0.22 | 0.036 | NO
43 | VAV1 | VAV1 | VAV1 | 15621 | -0.23 | 0.066 | NO
44 | ARHGAP9 | ARHGAP9 | ARHGAP9 | 17158 | -0.44 | 0.053 | NO

Figure S113. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS.

Figure S114. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME PRE NOTCH TRANSCRIPTION AND TRANSLATION

Table S58. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | PKP1 | PKP1 | PKP1 | 52 | 0.73 | 0.16 | YES
2 | GAS2 | GAS2 | GAS2 | 203 | 0.53 | 0.27 | YES
3 | MAPT | MAPT | MAPT | 1039 | 0.3 | 0.29 | YES
4 | OCLN | OCLN | OCLN | 1660 | 0.24 | 0.31 | YES
5 | DSP | DSP | DSP | 2554 | 0.17 | 0.3 | YES
6 | PTK2 | PTK2 | PTK2 | 3482 | 0.13 | 0.28 | YES
7 | PRKCQ | PRKCQ | PRKCQ | 3535 | 0.13 | 0.3 | YES
8 | CASP7 | CASP7 | CASP7 | 3747 | 0.12 | 0.32 | YES
9 | LMNA | LMNA | LMNA | 4167 | 0.1 | 0.32 | YES
10 | CASP6 | CASP6 | CASP6 | 4345 | 0.099 | 0.33 | YES
11 | DSG3 | DSG3 | DSG3 | 4557 | 0.092 | 0.34 | YES
12 | FNTA | FNTA | FNTA | 4670 | 0.089 | 0.35 | YES
13 | APC | APC | APC | 4782 | 0.086 | 0.36 | YES
14 | PLEC | PLEC | PLEC | 4826 | 0.085 | 0.38 | YES
15 | DSG2 | DSG2 | DSG2 | 5150 | 0.076 | 0.38 | NO
16 | TJP1 | TJP1 | TJP1 | 5585 | 0.064 | 0.37 | NO
17 | VIM | VIM | VIM | 5689 | 0.062 | 0.38 | NO
18 | TJP2 | TJP2 | TJP2 | 6133 | 0.052 | 0.37 | NO
19 | CTNNB1 | CTNNB1 | CTNNB1 | 6607 | 0.041 | 0.35 | NO
20 | SPTAN1 | SPTAN1 | SPTAN1 | 6978 | 0.034 | 0.34 | NO
21 | ROCK1 | ROCK1 | ROCK1 | 7401 | 0.025 | 0.32 | NO
22 | GSN | GSN | GSN | 7612 | 0.021 | 0.31 | NO
23 | ADD1 | ADD1 | ADD1 | 7751 | 0.018 | 0.31 | NO
24 | BCAP31 | BCAP31 | BCAP31 | 7765 | 0.018 | 0.31 | NO
25 | ACIN1 | ACIN1 | ACIN1 | 7816 | 0.017 | 0.31 | NO
26 | LOC647859 | LOC647859 | LOC647859 | 8390 | 0.0062 | 0.28 | NO
27 | PRKCD | PRKCD | PRKCD | 8643 | 0.0018 | 0.27 | NO
28 | BIRC2 | BIRC2 | BIRC2 | 9007 | -0.0047 | 0.25 | NO
29 | STK24 | STK24 | STK24 | 10334 | -0.028 | 0.18 | NO
30 | LMNB1 | LMNB1 | LMNB1 | 10977 | -0.04 | 0.16 | NO
31 | CASP3 | CASP3 | CASP3 | 11678 | -0.055 | 0.13 | NO
32 | SATB1 | SATB1 | SATB1 | 11813 | -0.058 | 0.14 | NO
33 | CDH1 | CDH1 | CDH1 | 11840 | -0.059 | 0.15 | NO
34 | DSG1 | DSG1 | DSG1 | 12436 | -0.073 | 0.13 | NO
35 | DBNL | DBNL | DBNL | 12513 | -0.076 | 0.14 | NO
36 | CASP8 | CASP8 | CASP8 | 12916 | -0.087 | 0.14 | NO
37 | MST4 | MST4 | MST4 | 14141 | -0.13 | 0.1 | NO
38 | BMX | BMX | BMX | 17539 | -0.53 | 0.032 | NO

Figure S115. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME PRE NOTCH TRANSCRIPTION AND TRANSLATION.

Figure S116. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME PRE NOTCH TRANSCRIPTION AND TRANSLATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME PRE NOTCH EXPRESSION AND PROCESSING

Table S59. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | DTX1 | DTX1 | DTX1 | 450 | 0.41 | 0.052 | YES
2 | MAML3 | MAML3 | MAML3 | 735 | 0.34 | 0.1 | YES
3 | MAML2 | MAML2 | MAML2 | 1501 | 0.25 | 0.11 | YES
4 | NOTCH3 | NOTCH3 | NOTCH3 | 1554 | 0.25 | 0.15 | YES
5 | HES1 | HES1 | HES1 | 1886 | 0.22 | 0.17 | YES
6 | JAG1 | JAG1 | JAG1 | 2003 | 0.21 | 0.2 | YES
7 | NOTCH1 | NOTCH1 | NOTCH1 | 2047 | 0.2 | 0.24 | YES
8 | PSEN2 | PSEN2 | PSEN2 | 2204 | 0.2 | 0.27 | YES
9 | DTX3 | DTX3 | DTX3 | 2687 | 0.17 | 0.27 | YES
10 | DTX4 | DTX4 | DTX4 | 3050 | 0.15 | 0.28 | YES
11 | CTBP2 | CTBP2 | CTBP2 | 3206 | 0.14 | 0.3 | YES
12 | NCSTN | NCSTN | NCSTN | 3242 | 0.14 | 0.32 | YES
13 | APH1A | APH1A | APH1A | 3648 | 0.12 | 0.32 | YES
14 | NOTCH2 | NOTCH2 | NOTCH2 | 3650 | 0.12 | 0.35 | YES
15 | DLL3 | DLL3 | DLL3 | 4612 | 0.091 | 0.31 | NO
16 | NCOR2 | NCOR2 | NCOR2 | 4640 | 0.09 | 0.32 | NO
17 | MAML1 | MAML1 | MAML1 | 5273 | 0.073 | 0.3 | NO
18 | KAT2A | KAT2A | KAT2A | 5366 | 0.07 | 0.31 | NO
19 | CREBBP | CREBBP | CREBBP | 5599 | 0.064 | 0.31 | NO
20 | KAT2B | KAT2B | KAT2B | 5825 | 0.059 | 0.31 | NO
21 | DVL2 | DVL2 | DVL2 | 5860 | 0.058 | 0.32 | NO
22 | EP300 | EP300 | EP300 | 5906 | 0.057 | 0.33 | NO
23 | JAG2 | JAG2 | JAG2 | 6124 | 0.052 | 0.32 | NO
24 | RBPJ | RBPJ | RBPJ | 6818 | 0.037 | 0.29 | NO
25 | CIR1 | CIR1 | CIR1 | 6997 | 0.033 | 0.29 | NO
26 | HDAC2 | HDAC2 | HDAC2 | 7338 | 0.026 | 0.28 | NO
27 | DTX3L | DTX3L | DTX3L | 7400 | 0.025 | 0.28 | NO
28 | HES5 | HES5 | HES5 | 7826 | 0.017 | 0.26 | NO
29 | MFNG | MFNG | MFNG | 7935 | 0.015 | 0.25 | NO
30 | DVL1 | DVL1 | DVL1 | 8145 | 0.011 | 0.24 | NO
31 | CTBP1 | CTBP1 | CTBP1 | 8727 | 0.00026 | 0.21 | NO
32 | RFNG | RFNG | RFNG | 9841 | -0.02 | 0.15 | NO
33 | PSEN1 | PSEN1 | PSEN1 | 10502 | -0.031 | 0.12 | NO
34 | DLL4 | DLL4 | DLL4 | 10597 | -0.033 | 0.12 | NO
35 | SNW1 | SNW1 | SNW1 | 10685 | -0.035 | 0.13 | NO
36 | DVL3 | DVL3 | DVL3 | 10964 | -0.04 | 0.12 | NO
37 | PSENEN | PSENEN | PSENEN | 11549 | -0.052 | 0.096 | NO
38 | LFNG | LFNG | LFNG | 11726 | -0.056 | 0.096 | NO
39 | HDAC1 | HDAC1 | HDAC1 | 11744 | -0.057 | 0.11 | NO
40 | ADAM17 | ADAM17 | ADAM17 | 12060 | -0.064 | 0.1 | NO
41 | NOTCH4 | NOTCH4 | NOTCH4 | 12559 | -0.077 | 0.087 | NO
42 | NUMB | NUMB | NUMB | 12827 | -0.085 | 0.089 | NO
43 | DTX2 | DTX2 | DTX2 | 13086 | -0.093 | 0.092 | NO
44 | NUMBL | NUMBL | NUMBL | 14356 | -0.14 | 0.048 | NO
45 | RBPJL | RBPJL | RBPJL | 14602 | -0.16 | 0.063 | NO
46 | PTCRA | PTCRA | PTCRA | 16455 | -0.32 | 0.022 | NO
47 | DLL1 | DLL1 | DLL1 | 16779 | -0.37 | 0.074 | NO

Figure S117. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME PRE NOTCH EXPRESSION AND PROCESSING.

Figure S118. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME PRE NOTCH EXPRESSION AND PROCESSING, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION

Table S60. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | DTX1 | DTX1 | DTX1 | 450 | 0.41 | 0.015 | YES
2 | TLE2 | TLE2 | TLE2 | 454 | 0.41 | 0.055 | YES
3 | HEY1 | HEY1 | HEY1 | 730 | 0.34 | 0.073 | YES
4 | MAML3 | MAML3 | MAML3 | 735 | 0.34 | 0.11 | YES
5 | MAMLD1 | MAMLD1 | MAMLD1 | 1011 | 0.3 | 0.12 | YES
6 | APH1B | APH1B | APH1B | 1235 | 0.28 | 0.14 | YES
7 | MAML2 | MAML2 | MAML2 | 1501 | 0.25 | 0.14 | YES
8 | NOTCH3 | NOTCH3 | NOTCH3 | 1554 | 0.25 | 0.17 | YES
9 | CCND1 | CCND1 | CCND1 | 1727 | 0.23 | 0.18 | YES
10 | HES1 | HES1 | HES1 | 1886 | 0.22 | 0.19 | YES
11 | JAG1 | JAG1 | JAG1 | 2003 | 0.21 | 0.2 | YES
12 | FURIN | FURIN | FURIN | 2148 | 0.2 | 0.22 | YES
13 | PSEN2 | PSEN2 | PSEN2 | 2204 | 0.2 | 0.23 | YES
14 | HDAC11 | HDAC11 | HDAC11 | 2444 | 0.18 | 0.24 | YES
15 | TLE4 | TLE4 | TLE4 | 2668 | 0.17 | 0.24 | YES
16 | HDAC5 | HDAC5 | HDAC5 | 2840 | 0.16 | 0.25 | YES
17 | NEURL | NEURL | NEURL | 2903 | 0.16 | 0.26 | YES
18 | DTX4 | DTX4 | DTX4 | 3050 | 0.15 | 0.26 | YES
19 | TP53 | TP53 | TP53 | 3221 | 0.14 | 0.27 | YES
20 | NCSTN | NCSTN | NCSTN | 3242 | 0.14 | 0.28 | YES
21 | EIF2C2 | EIF2C2 | EIF2C2 | 3291 | 0.14 | 0.29 | YES
22 | APH1A | APH1A | APH1A | 3648 | 0.12 | 0.28 | YES
23 | NOTCH2 | NOTCH2 | NOTCH2 | 3650 | 0.12 | 0.3 | YES
24 | HDAC7 | HDAC7 | HDAC7 | 3984 | 0.11 | 0.29 | NO
25 | TLE1 | TLE1 | TLE1 | 4408 | 0.097 | 0.27 | NO
26 | NCOR2 | NCOR2 | NCOR2 | 4640 | 0.09 | 0.27 | NO
27 | TNRC6C | TNRC6C | TNRC6C | 4910 | 0.082 | 0.26 | NO
28 | E2F3 | E2F3 | E2F3 | 5132 | 0.076 | 0.26 | NO
29 | MAML1 | MAML1 | MAML1 | 5273 | 0.073 | 0.26 | NO
30 | HDAC4 | HDAC4 | HDAC4 | 5359 | 0.07 | 0.26 | NO
31 | KAT2A | KAT2A | KAT2A | 5366 | 0.07 | 0.26 | NO
32 | CNTN1 | CNTN1 | CNTN1 | 5471 | 0.067 | 0.27 | NO
33 | NCOR1 | NCOR1 | NCOR1 | 5489 | 0.067 | 0.27 | NO
34 | CREBBP | CREBBP | CREBBP | 5599 | 0.064 | 0.27 | NO
35 | EIF2C4 | EIF2C4 | EIF2C4 | 5799 | 0.059 | 0.27 | NO
36 | KAT2B | KAT2B | KAT2B | 5825 | 0.059 | 0.27 | NO
37 | EP300 | EP300 | EP300 | 5906 | 0.057 | 0.27 | NO
38 | JAG2 | JAG2 | JAG2 | 6124 | 0.052 | 0.26 | NO
39 | ADAM10 | ADAM10 | ADAM10 | 6200 | 0.05 | 0.26 | NO
40 | HEYL | HEYL | HEYL | 6272 | 0.048 | 0.27 | NO
41 | TNRC6A | TNRC6A | TNRC6A | 6407 | 0.045 | 0.26 | NO
42 | FBXW7 | FBXW7 | FBXW7 | 6548 | 0.042 | 0.26 | NO
43 | E2F1 | E2F1 | E2F1 | 6555 | 0.042 | 0.26 | NO
44 | JUN | JUN | JUN | 6765 | 0.038 | 0.26 | NO
45 | RBPJ | RBPJ | RBPJ | 6818 | 0.037 | 0.26 | NO
46 | HDAC10 | HDAC10 | HDAC10 | 6931 | 0.035 | 0.25 | NO
47 | B4GALT1 | B4GALT1 | B4GALT1 | 7137 | 0.03 | 0.24 | NO
48 | MIB1 | MIB1 | MIB1 | 7331 | 0.026 | 0.24 | NO
49 | HDAC2 | HDAC2 | HDAC2 | 7338 | 0.026 | 0.24 | NO
50 | HIF1A | HIF1A | HIF1A | 7342 | 0.026 | 0.24 | NO
51 | SKP1 | SKP1 | SKP1 | 7525 | 0.023 | 0.23 | NO
52 | HES5 | HES5 | HES5 | 7826 | 0.017 | 0.22 | NO
53 | HDAC8 | HDAC8 | HDAC8 | 7924 | 0.015 | 0.21 | NO
54 | MFNG | MFNG | MFNG | 7935 | 0.015 | 0.21 | NO
55 | HEY2 | HEY2 | HEY2 | 8335 | 0.0074 | 0.19 | NO
56 | POFUT1 | POFUT1 | POFUT1 | 8600 | 0.0026 | 0.18 | NO
57 | ATP2A2 | ATP2A2 | ATP2A2 | 8680 | 0.0012 | 0.17 | NO
58 | TNRC6B | TNRC6B | TNRC6B | 8817 | -0.0011 | 0.17 | NO
59 | RPS27A | RPS27A | RPS27A | 9002 | -0.0045 | 0.16 | NO
60 | TBL1X | TBL1X | TBL1X | 9567 | -0.014 | 0.13 | NO
61 | TMED2 | TMED2 | TMED2 | 9761 | -0.018 | 0.12 | NO
62 | RFNG | RFNG | RFNG | 9841 | -0.02 | 0.12 | NO
63 | ARRB1 | ARRB1 | ARRB1 | 9925 | -0.021 | 0.11 | NO
64 | HDAC6 | HDAC6 | HDAC6 | 9927 | -0.021 | 0.12 | NO
65 | CUL1 | CUL1 | CUL1 | 10217 | -0.026 | 0.1 | NO
66 | RAB6A | RAB6A | RAB6A | 10279 | -0.027 | 0.1 | NO
67 | HDAC9 | HDAC9 | HDAC9 | 10351 | -0.028 | 0.1 | NO
68 | PSEN1 | PSEN1 | PSEN1 | 10502 | -0.031 | 0.094 | NO
69 | UBA52 | UBA52 | UBA52 | 10586 | -0.033 | 0.093 | NO
70 | DLL4 | DLL4 | DLL4 | 10597 | -0.033 | 0.096 | NO
71 | SNW1 | SNW1 | SNW1 | 10685 | -0.035 | 0.094 | NO
72 | EIF2C1 | EIF2C1 | EIF2C1 | 10809 | -0.037 | 0.091 | NO
73 | DLK1 | DLK1 | DLK1 | 10867 | -0.038 | 0.092 | NO
74 | HDAC3 | HDAC3 | HDAC3 | 11172 | -0.045 | 0.079 | NO
75 | CCNC | CCNC | CCNC | 11183 | -0.045 | 0.083 | NO
76 | PSENEN | PSENEN | PSENEN | 11549 | -0.052 | 0.068 | NO
77 | LFNG | LFNG | LFNG | 11726 | -0.056 | 0.063 | NO
78 | HDAC1 | HDAC1 | HDAC1 | 11744 | -0.057 | 0.068 | NO
79 | RBX1 | RBX1 | RBX1 | 11908 | -0.06 | 0.065 | NO
80 | ADAM17 | ADAM17 | ADAM17 | 12060 | -0.064 | 0.062 | NO
81 | TBL1XR1 | TBL1XR1 | TBL1XR1 | 12105 | -0.065 | 0.066 | NO
82 | SEL1L | SEL1L | SEL1L | 12294 | -0.069 | 0.063 | NO
83 | MOV10 | MOV10 | MOV10 | 12298 | -0.069 | 0.069 | NO
84 | TLE3 | TLE3 | TLE3 | 12478 | -0.074 | 0.066 | NO
85 | NOTCH4 | NOTCH4 | NOTCH4 | 12559 | -0.077 | 0.069 | NO
86 | TFDP1 | TFDP1 | TFDP1 | 12753 | -0.083 | 0.067 | NO
87 | NUMB | NUMB | NUMB | 12827 | -0.085 | 0.071 | NO
88 | DTX2 | DTX2 | DTX2 | 13086 | -0.093 | 0.066 | NO
89 | ARRB2 | ARRB2 | ARRB2 | 13205 | -0.097 | 0.068 | NO
90 | MIB2 | MIB2 | MIB2 | 13221 | -0.097 | 0.077 | NO
91 | ST3GAL6 | ST3GAL6 | ST3GAL6 | 13407 | -0.1 | 0.077 | NO
92 | MYC | MYC | MYC | 13449 | -0.1 | 0.085 | NO
93 | ATP2A1 | ATP2A1 | ATP2A1 | 13865 | -0.12 | 0.073 | NO
94 | CDK8 | CDK8 | CDK8 | 14027 | -0.13 | 0.077 | NO
95 | ST3GAL3 | ST3GAL3 | ST3GAL3 | 14110 | -0.13 | 0.085 | NO
96 | EIF2C3 | EIF2C3 | EIF2C3 | 14690 | -0.16 | 0.068 | NO
97 | ATP2A3 | ATP2A3 | ATP2A3 | 15571 | -0.22 | 0.041 | NO
98 | DLL1 | DLL1 | DLL1 | 16779 | -0.37 | 0.01 | NO
99 | DNER | DNER | DNER | 17860 | -0.66 | 0.014 | NO

Figure S119. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION.

Figure S120. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

For the top enriched genes, if you want to check whether they are

- up-regulated, please check the list of up-regulated genes

- down-regulated, please check the list of down-regulated genes

Expression level

For the top enriched genes, if you want to check whether they are

- highly expressed genes, please check the list of high (top 30%) expressed genes

- low expressed genes, please check the list of low (bottom 30%) expressed genes

An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap

Significant gene list

For the top enriched genes, if you want to check whether they are

- significantly differently expressed genes by eBayes lm fit, please check the list of significant genes

Methods & Data
Input

- Gene set database = c2.cp.v4.0.symbols.gmt

- Expression data file = CHOL-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

- Phenotype data file = CHOL-TP.mergedcluster.txt

GSEA analysis

For the Gene Set Enrichment Analysis (GSEA), Broad GSEA-P-R.1.0 version is used with class2: canonical pathways geneses from MSigDB. Further details about statistics are available inThe Broad GSEA website.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Subramanian, A. et al, Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles., Proc. Natl. Acad. Sci. USA 102(43) (2005)
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